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FreeBSD Ports: Biology

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Software related to biology.

CheckM-1.0.18
Quality assessment tool for the microbial genomes
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: atk-2.28.1, avahi-app-0.7_2, binutils-2.32_1,1, blas-3.5.0_6, ca_root_nss-3.46, cairo-1.16.0,2, cblas-1.0_12, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gcc9-9.2.0, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_8, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libglade2-2.6.4_9, libiconv-1.14_11, libidn2-2.2.0, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.5.1_1, openblas-0.2.20_10,1, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, pixman-0.38.4, png-1.6.37, py27-DendroPy-4.4.0, py27-backports-1, py27-backports.functools_lru_cache-1.5, py27-dateutil-2.8.0, py27-gobject-2.28.6_8, py27-gtk2-2.24.0_5, py27-kiwisolver-1.1.0, py27-matplotlib-2.2.4_1, py27-pysam-0.15.3, py27-scipy-1.2.2_1, py35-setuptools-41.2.0, py36-cairo-1.18.1_1, py36-cycler-0.10.0, py36-cython-0.29_1, py36-pyparsing-2.4.1.1, py36-pytz-2019.2,1, py36-six-1.12.0, py36-tkinter-3.6.9_6, py36-tornado-5.1.1, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, shared-mime-info-1.10_1, suitesparse-5.2.0_4, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xmlcatmgr-2.2_2, xorg-fonts-truetype-7.7_1, xorgproto-2019.1
Also listed in: Python

FastTree-2.1.10_4
Approximately-maximum-likelihood phylogenetic trees from alignments
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2

GroopM-0.3.4_2
Metagenomic binning suite
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: atk-2.28.1, avahi-app-0.7_2, binutils-2.32_1,1, blas-3.5.0_6, ca_root_nss-3.46, cairo-1.16.0,2, cblas-1.0_12, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gcc9-9.2.0, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hdf-szip-2.1.1, hdf5-1.10.5_2, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_8, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libglade2-2.6.4_9, libiconv-1.14_11, libidn2-2.2.0, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, lzo2-2.10_1, mesa-libs-18.3.2_1, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.5.1_1, openblas-0.2.20_10,1, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, pixman-0.38.4, png-1.6.37, py27-backports-1, py27-backports.functools_lru_cache-1.5, py27-dateutil-2.8.0, py27-gobject-2.28.6_8, py27-gtk2-2.24.0_5, py27-kiwisolver-1.1.0, py27-matplotlib-2.2.4_1, py27-scipy-1.2.2_1, py27-tables-3.5.2_1, py35-setuptools-41.2.0, py36-cairo-1.18.1_1, py36-cycler-0.10.0, py36-numexpr-2.7.0, py36-pyparsing-2.4.1.1, py36-pytz-2019.2,1, py36-six-1.12.0, py36-tkinter-3.6.9_6, py36-tornado-5.1.1, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, shared-mime-info-1.10_1, suitesparse-5.2.0_4, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, ucl-1.03_5, wayland-1.16.0_1, xmlcatmgr-2.2_2, xorg-fonts-truetype-7.7_1, xorgproto-2019.1
Also listed in: Python

InsightToolkit-5.0.1
Insight Toolkit
Long description | Changes | Main Web Site
Maintained by: woodsb02@FreeBSD.org
Requires: binutils-2.32_1,1, ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, eigen-3.3.7, expat-2.2.6_1, fftw-2.1.5_22, gcc9-9.2.0, gdcm-3.0.1, gettext-runtime-0.20.1, gmp-6.1.2_1, googletest-1.8.1_3, hdf-szip-2.1.1, hdf5-1.10.5_2, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, jsoncpp-1.8.1_7, lcms2-2.9, libarchive-3.4.0,1, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.0.2, ninja-1.9.0,2, openjpeg-2.3.1, pkgconf-1.6.3,1, png-1.6.37, python36-3.6.9, readline-8.0.0, rhash-1.3.5, tiff-4.0.10_1
Also listed in: Science

Jellyfish-2.2.10_7
Fast, memory-efficient counting of k-mers in DNA
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, ca_root_nss-3.46, curl-7.66.0, gettext-runtime-0.20.1, gettext-tools-0.20.1_1, gmake-4.2.1_3, htslib-1.9, indexinfo-0.3.1, libedit-3.1.20190324,1, libffi-3.2.1_3, libnghttp2-1.39.2, libtextstyle-0.20.1, libtool-2.4.6_1, libunwind-20170615, libyaml-0.2.2, m4-1.4.18_1,1, perl5-5.30.0, pkgconf-1.6.3,1, ruby-2.6.4,1, yaggo-1.5.9

abyss-2.1.5_4
Assembly By Short Sequences: parallel, paired-end sequence assembler
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: bash-5.0.11, boost-libs-1.71.0, gettext-runtime-0.20.1, ghc-8.6.5_3, gmake-4.2.1_3, gmp-6.1.2_1, hs-pandoc-2.7.2_1, icu-64.2,1, indexinfo-0.3.1, libffi-3.2.1_3, libiconv-1.14_11, openmp-8.0.0_2, readline-8.0.0, sqlite3-3.29.0

afni-19.1.20_2
Advanced Functional Neuro Imaging
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: R-3.6.1_1, avahi-app-0.7_2, binutils-2.32_1,1, ca_root_nss-3.46, cairo-1.16.0,2, cups-2.2.12, curl-7.66.0, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, endian-1.1, expat-2.2.6_1, f2c-20060810_6, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gcc9-9.2.0, gdbm-1.18.1_1, gettext-runtime-0.20.1, gettext-tools-0.20.1_1, ghostscript9-agpl-base-9.27_2, glib-2.56.3_6,1, gmake-4.2.1_3, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gsl-2.5_1, harfbuzz-2.6.1_1, hdf-szip-2.1.1, hdf5-1.10.5_2, icu-64.2,1, indexinfo-0.3.1, jasper-1.900.1_17, jbig2dec-0.16, jbigkit-2.1_1, jpeg-turbo-2.0.2, libGLU-9.0.0_3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_2,2, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXmu-1.1.3,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libiconv-1.14_11, libidn-1.35, libidn2-2.2.0, libnghttp2-1.39.2, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libtextstyle-0.20.1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, m4-1.4.18_1,1, mesa-libs-18.3.2_1, mkfontscale-1.2.1, mpc-1.1.0_2, mpeg_encode-1.5b, mpfr-4.0.2, netcdf-4.7.1, netcdf-fortran-4.5.1, netpbm-10.87.02, nettle-3.5.1_1, open-motif-2.3.8, openmp-8.0.0_2, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, perl5-5.30.0, pixman-0.38.4, pkgconf-1.6.3,1, png-1.6.37, poppler-data-0.4.9, python36-3.6.9, qhull5-1.0_3, readline-8.0.0, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xbitmaps-1.1.2, xorg-fonts-truetype-7.7_1, xorgproto-2019.1
Also listed in: Science, Graphics, Perl5, Python

artemis-17.0.1.11
DNA sequence viewer and annotation tool
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, bash-5.0.11, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, gettext-runtime-0.20.1, giflib-5.1.9, gmake-4.2.1_3, indexinfo-0.3.1, java-zoneinfo-2019.b, javavmwrapper-2.7.3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, mkfontscale-1.2.1, openjdk8-8.222.10.1_2, xorgproto-2019.1
Also listed in: Java

avida-2.12.4
Auto-adaptive genetic system designed for ALife research
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, gettext-runtime-0.20.1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.9, readline-8.0.0, rhash-1.3.5

babel-1.6_4
Converts among various molecular file formats
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Also listed in: Converters

bamtools-2.5.1
API and toolkit for handling BAM files
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, gettext-runtime-0.20.1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.9, readline-8.0.0, rhash-1.3.5

bcftools-1.9
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, ca_root_nss-3.46, curl-7.66.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gsl-2.5_1, htslib-1.9, indexinfo-0.3.1, libnghttp2-1.39.2, m4-1.4.18_1,1, perl5-5.30.0

bedtools-2.29.0
Toolset for genome set arithmetic such as intersect, union
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, python36-3.6.9, readline-8.0.0

biococoa-2.2.2_6
Bioinformatics framework
Long description | Changes | Main Web Site
Maintained by: theraven@FreeBSD.org
Requires: avahi-app-0.7_2, ca_root_nss-3.46, cairo-1.16.0,2, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, expat-2.2.6_1, flac-1.3.3, flite-2.1, fontconfig-2.12.6,1, freetype2-2.10.1, gdbm-1.18.1_1, gettext-runtime-0.20.1, giflib-5.1.9, glib-2.56.3_6,1, gmake-4.2.1_3, gmp-6.1.2_1, gnome_subr-1.0, gnustep-back-0.27.0, gnustep-base-1.26.0_2, gnustep-gui-0.27.0_1, gnustep-make-2.7.0_3, gnutls-3.6.9, gobject-introspection-1.56.1,1, icu-64.2,1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXmu-1.1.3,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libao-1.2.0_4, libdaemon-0.14_1, libdrm-2.4.99,1, libedit-3.1.20190324,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libgcrypt-1.8.5, libgpg-error-1.36, libiconv-1.14_11, libidn2-2.2.0, libobjc2-2.0_1, libogg-1.3.4,4, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libsndfile-1.0.28_2, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libvorbis-1.3.6,3, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, libxslt-1.1.33, llvm70-7.0.1_4, mesa-libs-18.3.2_1, nettle-3.5.1_1, p11-kit-0.23.17, pciids-20190725, pcre-8.43_2, perl5-5.30.0, pixman-0.38.4, png-1.6.37, python27-2.7.16_1, python36-3.6.9, readline-8.0.0, tiff-4.0.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xorgproto-2019.1
Also listed in: Gnustep

bolt-lmm-2.3.4_1
Mixed model association testing and variance component analysis
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, boehm-gc-8.0.4_1, boehm-gc-threaded-8.0.4_1, boost-libs-1.71.0, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, guile2-2.2.6_1, icu-64.2,1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, libltdl-2.4.6, libunistring-0.9.10_1, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, nlopt-2.6.1_2, openblas-0.2.20_10,1, py35-setuptools-41.2.0, py37-numpy-1.16.5,1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4

bowtie-1.1.2_9
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, libffi-3.2.1_3, mpc-1.1.0_2, mpfr-4.0.2, perl5-5.30.0, python36-3.6.9, readline-8.0.0

bowtie2-2.3.5.1
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: bash-5.0.11, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, perl5-5.30.0, python36-3.6.9, readline-8.0.0, tbb-2019.5
Also listed in: Perl5, Python

bwa-0.7.17
Burrows-Wheeler sequence aligner
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, perl5-5.30.0

canu-1.8_5
Single molecule sequence assembler
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ORBit2-2.14.19_2, alsa-lib-1.1.2_2, atk-2.28.1, avahi-app-0.7_2, binutils-2.32_1,1, boost-libs-1.71.0, ca_root_nss-3.46, cairo-1.16.0,2, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, dconf-0.28.0, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gcc9-9.2.0, gconf2-3.2.6_5, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, giflib-5.1.9, glib-2.56.3_6,1, gmake-4.2.1_3, gmp-6.1.2_1, gnome_subr-1.0, gnuplot-5.2.7_1, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gstreamer-0.10.36_6, gstreamer-plugins-0.10.36_12,3, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, icu-64.2,1, indexinfo-0.3.1, java-zoneinfo-2019.b, javavmwrapper-2.7.3, jbigkit-2.1_1, jpeg-turbo-2.0.2, libGLU-9.0.0_3, libICE-1.0.10,1, libIDL-0.8.14_4, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXv-1.0.11_2,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libedit-3.1.20190324,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libgd-2.2.5_1,1, libiconv-1.14_11, libidn2-2.2.0, libinotify-20180201_1, libmspack-0.9.1, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, lua53-5.3.5_3, mesa-libs-18.3.2_1, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.5.1_1, nspr-4.22, openjdk8-8.222.10.1_2, orc-0.4.28, p11-kit-0.23.17, pango-1.42.4_3, pangox-compat-0.0.2_2, pciids-20190725, pcre-8.43_2, perl5-5.30.0, pixman-0.38.4, png-1.6.37, polkit-0.114_3, python36-3.6.9, readline-8.0.0, shared-mime-info-1.10_1, spidermonkey52-52.9.0_4, tex-kpathsea-6.2.1_2, tiff-4.0.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.3_1, wx28-gtk2-2.8.12_8, wx28-gtk2-common-2.8.12_8, xorg-fonts-truetype-7.7_1, xorgproto-2019.1
Also listed in: Java, Perl5

cd-hit-4.8.1_1
Clustering and comparing protein or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2

cdbfasta-2010.07.22
Fast indexing and retrieval of FASTA records from flat file databases
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

chemeq-1.50_2
Outputs LaTeX code for chemical reaction
Long description | Changes
Maintained by: ports@FreeBSD.org
Requires: bison-3.4.1,1, gettext-runtime-0.20.1, indexinfo-0.3.1, libtextstyle-0.20.1, m4-1.4.18_1,1
Also listed in: Textproc

clustal-omega-1.2.4
Multiple alignment of nucleic acid and protein, replaces clustalw
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: argtable-2.13_2

clustalw-2.1_2
Multiple alignment program for DNA or proteins
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

consed-27.0
Graphical tool for editing Phrap assemblies
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: linux-c7-expat-2.1.0_2, linux-c7-fontconfig-2.13.0, linux-c7-freetype-2.8, linux-c7-libpng-1.5.13_2, linux-c7-xorg-libs-7.7_7, linux_base-c7-7.6.1810_7, perl5-5.30.0, phrap-1.090518, phred-0.020425.c

cufflinks-2.2.1.83_1
Cufflinks assembles transcripts, estimates their abundance, etc
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, boost-libs-1.71.0, ca_root_nss-3.46, curl-7.66.0, eigen-3.3.7, gettext-runtime-0.20.1, gmake-4.2.1_3, htslib-1.9, icu-64.2,1, indexinfo-0.3.1, libffi-3.2.1_3, libnghttp2-1.39.2, m4-1.4.18_1,1, perl5-5.30.0, python36-3.6.9, readline-8.0.0

cycle-0.3.1_11
Calendar program for women
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ORBit2-2.14.19_2, adwaita-icon-theme-3.28.0, argyllcms-1.9.2_5, at-spi2-atk-2.26.2, at-spi2-core-2.28.0, atk-2.28.1, avahi-app-0.7_2, brotli-1.0.7_2,1, ca_root_nss-3.46, cairo-1.16.0,2, colord-1.3.5, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, dconf-0.28.0, dejavu-2.37_1, enchant2-2.2.3_4, encodings-1.0.5,1, expat-2.2.6_1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gconf2-3.2.6_5, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, geoclue-2.4.7, gettext-runtime-0.20.1, giflib-5.1.9, glib-2.56.3_6,1, glib-networking-2.56.1_2, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphene-1.8.2_1, graphite2-1.3.13_1, gsettings-desktop-schemas-3.28.1, gstreamer1-1.14.4, gstreamer1-plugins-1.14.4_2, gstreamer1-plugins-bad-1.14.4, gstreamer1-plugins-gl-1.14.4_2, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, gtk3-3.24.10_1, harfbuzz-2.6.1_1, harfbuzz-icu-2.6.1_1, hicolor-icon-theme-0.17, hunspell-1.7.0_2, hyphen-2.8.8, icu-64.2,1, indexinfo-0.3.1, iso-codes-4.2, jbigkit-2.1_1, jpeg-turbo-2.0.2, json-glib-1.4.2, lcms2-2.9, libGLU-9.0.0_3, libICE-1.0.10,1, libIDL-0.8.14_4, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libcroco-0.6.12, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libepoxy-1.5.2, libffi-3.2.1_3, libfontenc-1.1.4, libgcrypt-1.8.5, libgpg-error-1.36, libgsf-1.14.44, libiconv-1.14_11, libidn2-2.2.0, libmspack-0.9.1, libnotify-0.7.7_1, libpaper-1.1.24.4, libpciaccess-0.16, libproxy-0.4.15, libpthread-stubs-0.4, librsvg2-2.40.20, libsecret-0.18.6_1, libsoup-2.62.3, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxkbcommon-0.8.4, libxml2-2.9.9, libxshmfence-1.3, libxslt-1.1.33, mesa-libs-18.3.2_1, mkfontscale-1.2.1, nettle-3.5.1_1, nspr-4.22, openjpeg-2.3.1, orc-0.4.28, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, perl5-5.30.0, pixman-0.38.4, png-1.6.37, polkit-0.114_3, py27-wxPython-common-3.0.2.0_8, py27-wxPython30-3.0.2.0_8, py35-setuptools-41.2.0, py36-cairo-1.18.1_1, py36-gobject3-3.28.3, pygobject3-common-3.28.3, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, readline-8.0.0, shared-mime-info-1.10_1, spidermonkey52-52.9.0_4, sqlite3-3.29.0, tiff-4.0.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, wayland-protocols-1.17, webkit2-gtk3-2.24.4, webp-1.0.3_1, woff2-1.0.2_4, wx30-gtk3-3.0.4_8, xkeyboard-config-2.27, xorg-fonts-truetype-7.7_1, xorgproto-2019.1
Also listed in: Deskutils, Python

cytoscape-3.6.1
Software to visualize molecular interaction networks, gene expression
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, bash-5.0.11, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, gettext-runtime-0.20.1, giflib-5.1.9, indexinfo-0.3.1, java-zoneinfo-2019.b, javavmwrapper-2.7.3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, maven-3.6.1, maven-wrapper-1_2, mkfontscale-1.2.1, openjdk8-8.222.10.1_2, xorgproto-2019.1
Also listed in: Java

dDocent-2.7.8_1
Bash pipeline for RAD sequencing
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ORBit2-2.14.19_2, alsa-lib-1.1.2_2, atk-2.28.1, avahi-app-0.7_2, bamtools-2.5.1, bash-5.0.11, bedtools-2.29.0, binutils-2.32_1,1, bwa-0.7.17, ca_root_nss-3.46, cairo-1.16.0,2, cd-hit-4.8.1_1, coreutils-8.31, cups-2.2.12, curl-7.66.0, dbus-1.12.12, dbus-glib-0.110, dconf-0.28.0, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, fastahack-g20160702, fastp-0.20.0_1, filevercmp-g20151117, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freebayes-1.2.0_2, freetype2-2.10.1, fribidi-0.19.7, fsom-g20151117_2, gawk-5.0.0, gcc9-9.2.0, gconf2-3.2.6_5, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, giflib-5.1.9, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnuplot-5.2.7_1, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gstreamer-0.10.36_6, gstreamer-plugins-0.10.36_12,3, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, htslib-1.9, icu-64.2,1, indexinfo-0.3.1, intervaltree-g20151213_2, java-zoneinfo-2019.b, javavmwrapper-2.7.3, jbigkit-2.1_1, jpeg-turbo-2.0.2, jsoncpp-1.8.1_7, libGLU-9.0.0_3, libICE-1.0.10,1, libIDL-0.8.14_4, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXv-1.0.11_2,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libedit-3.1.20190324,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libgd-2.2.5_1,1, libiconv-1.14_11, libidn2-2.2.0, libinotify-20180201_1, libmspack-0.9.1, libnghttp2-1.39.2, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libsigsegv-2.12, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, lua53-5.3.5_3, mawk-1.3.4.20161120, mesa-libs-18.3.2_1, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, multichoose-1.0.3.2, nettle-3.5.1_1, nspr-4.22, openjdk8-8.222.10.1_2, orc-0.4.28, p11-kit-0.23.17, pango-1.42.4_3, pangox-compat-0.0.2_2, parallel-20180922, pciids-20190725, pcre-8.43_2, pear-merger-0.9.6, perl5-5.30.0, pixman-0.38.4, png-1.6.37, polkit-0.114_3, python36-3.6.9, rainbow-2.0.4, readline-8.0.0, samtools-1.9, seqtk-1.2.8, shared-mime-info-1.10_1, smithwaterman-g20160702, spidermonkey52-52.9.0_4, stacks-2.4_1, tabixpp-1.0.0.10, tex-kpathsea-6.2.1_2, tiff-4.0.10_1, tpm-emulator-0.7.4_2, trimadap-0.1.3, trimmomatic-0.39, trousers-0.3.14_2, unzip-6.0_8, vcflib-1.0.0.r1.130, vcftools-0.1.16, wayland-1.16.0_1, webp-1.0.3_1, wx28-gtk2-2.8.12_8, wx28-gtk2-common-2.8.12_8, xorg-fonts-truetype-7.7_1, xorgproto-2019.1
Also listed in: Java, Perl5, Python

diamond-0.9.25
BLAST-compatible local sequence aligner
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, gettext-runtime-0.20.1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.9, readline-8.0.0, rhash-1.3.5

dsr-pdb-1.0.3_4
Simple C++ PDB reader (reads the protein description format)
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: boost-libs-1.71.0, gettext-runtime-0.20.1, gmake-4.2.1_3, icu-64.2,1, indexinfo-0.3.1

emboss-6.6.0_3
Collection of open source tools for genetic sequence analysis
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: clustalw-2.1_2, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, gettext-runtime-0.20.1, giflib-5.1.9, gmake-4.2.1_3, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXaw-1.0.13_2,2, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.2_3, libXmu-1.1.3,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXrender-0.9.10_2, libXt-1.2.0,1, libgd-2.2.5_1,1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, open-motif-2.3.8, png-1.6.37, primer3-2.3.6, tiff-4.0.10_1, webp-1.0.3_1, xbitmaps-1.1.2, xorgproto-2019.1

exonerate-2.4.0
Generic tool for sequence alignment
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: gettext-runtime-0.20.1, glib-2.56.3_6,1, indexinfo-0.3.1, libffi-3.2.1_3, libiconv-1.14_11, libxml2-2.9.9, pcre-8.43_2, pkgconf-1.6.3,1, python36-3.6.9, readline-8.0.0

fasta-21.1.1
Collection of programs for searching DNA and protein databases
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

fasta3-36.3.8
Collection of programs for searching DNA and protein databases
Long description | Changes | Main Web Site
Maintained by: wendell@bsd.com.br

fastahack-g20160702
Utility for indexing and sequence extraction from FASTA files
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

fastdnaml-1.2.2_2
Faster DNAML, makes phylogenetic trees using maximum likelihood
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

fastool-0.1.4
Simple and quick FastQ and FastA tool for file reading and conversion
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

fastp-0.20.0_1
Ultra-fast all-in-one FASTQ preprocessor
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

fastqc-0.11.5
Quality control tool for high throughput sequence data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: alsa-lib-1.1.2_2, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, giflib-5.1.9, java-zoneinfo-2019.b, javavmwrapper-2.7.3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, mkfontscale-1.2.1, openjdk8-8.222.10.1_2, perl5-5.30.0, xorgproto-2019.1
Also listed in: Java, Perl5

fastx_toolkit-0.0.14
CLI tools for Short-Reads FASTA/FASTQ files preprocessing
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, indexinfo-0.3.1, libgtextutils-0.7, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.30.0, pkgconf-1.6.3,1

figtree-1.4.4
Graphical viewer of phylogenetic trees
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, apache-ant-1.10.6, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, giflib-5.1.9, java-zoneinfo-2019.b, javavmwrapper-2.7.3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, mkfontscale-1.2.1, openjdk8-8.222.10.1_2, xorgproto-2019.1
Also listed in: Java

fluctuate-1.40
Program to fit population models
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

freebayes-1.2.0_2
Bayesian haplotype-based polymorphism discovery and genotyping
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

garlic-1.6_1
Molecular viewer, editor, and visualization program
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, xorgproto-2019.1

gatk-4.1.2.0.43
Variant discovery in high-throughput sequencing data
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, gettext-runtime-0.20.1, giflib-5.1.9, gradle-5.0, indexinfo-0.3.1, java-zoneinfo-2019.b, javavmwrapper-2.7.3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, mkfontscale-1.2.1, openjdk8-8.222.10.1_2, xorgproto-2019.1
Also listed in: Java

gemma-0.98.1_1
Genome-wide Efficient Mixed Model Association
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, cblas-1.0_12, eigen-3.3.7, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, gsl-2.5_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1

gff2ps-0.98l
Converts gff-formated genomic data-sets to PostScript
Long description | Changes | Main Web Site
Maintained by: egypcio@FreeBSD.org
Requires: bash-5.0.11, gawk-5.0.0, gettext-runtime-0.20.1, indexinfo-0.3.1, libsigsegv-2.12, readline-8.0.0

gmap-2015.09.21
Genomic Mapping and Alignment Program for mRNA and EST Sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, perl5-5.30.0

gperiodic-3.0.3
Displays a periodic table of the elements
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: atk-2.28.1, avahi-app-0.7_2, ca_root_nss-3.46, cairo-1.16.0,2, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, gettext-tools-0.20.1_1, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libiconv-1.14_11, libidn2-2.2.0, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libtextstyle-0.20.1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, mkfontscale-1.2.1, nettle-3.5.1_1, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, pixman-0.38.4, pkgconf-1.6.3,1, png-1.6.37, python36-3.6.9, readline-8.0.0, shared-mime-info-1.10_1, tiff-4.0.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xorg-fonts-truetype-7.7_1, xorgproto-2019.1

graphlan-1.1.3
High-quality circular representations of taxonomic, phylogenetic trees
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, python27-2.7.16_1, readline-8.0.0

grappa-2.0
Genome Rearrangements Analysis and Phylogeny Software
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

hhsuite-3.2.0_1
Remote protein homology detection suite
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, hdf-szip-2.1.1, hdf5-1.10.5_2, hwloc-1.11.11, indexinfo-0.3.1, json-c-0.13.1_1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libedit-3.1.20190324,1, libevent-2.1.11, libffi-3.2.1_3, libltdl-2.4.6, liblz4-1.9.2,1, libnghttp2-1.39.2, libpciaccess-0.16, libsysinfo-0.0.3_2, libuv-1.32.0, libxml2-2.9.9, lua52-5.2.4, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.0.2, munge-0.5.13_1, ninja-1.9.0,2, openmp-8.0.0_2, openmpi-1.10.7_7, pciids-20190725, perl5-5.30.0, python36-3.6.9, readline-8.0.0, rhash-1.3.5, slurm-wlm-19.05.1.2_2
Also listed in: Science

hisat2-2.1.0.23
Alignment program for mapping next-generation sequencing reads
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, perl5-5.30.0, python36-3.6.9, readline-8.0.0
Also listed in: Perl5, Python

hmmer-3.2.1_1
Profile hidden Markov models for biological sequence analysis
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

htslib-1.9
C library for high-throughput sequencing data formats
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, ca_root_nss-3.46, curl-7.66.0, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libnghttp2-1.39.2, m4-1.4.18_1,1, perl5-5.30.0
Also listed in: Devel

hyphy-2.3.14.16_2
Hypothesis testing using Phylogenies
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, gettext-runtime-0.20.1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.9, readline-8.0.0, rhash-1.3.5

igv-2.5.3
Visualization tool for genomic datasets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: adwaita-icon-theme-3.28.0, alsa-lib-1.1.2_2, argyllcms-1.9.2_5, at-spi2-atk-2.26.2, at-spi2-core-2.28.0, atk-2.28.1, avahi-app-0.7_2, ca_root_nss-3.46, cairo-1.16.0,2, colord-1.3.5, cups-2.2.12, dav1d-0.4.0, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, ffmpeg-4.2.1_1,1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, giflib-5.1.9, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, gradle4-4.10.3, graphite2-1.3.13_1, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, gtk3-3.24.10_1, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, icu-64.2,1, indexinfo-0.3.1, java-zoneinfo-2019.b, javavmwrapper-2.7.3, jbigkit-2.1_1, jpeg-turbo-2.0.2, lcms2-2.9, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libcroco-0.6.12, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libepoxy-1.5.2, libffi-3.2.1_3, libfontenc-1.1.4, libgcrypt-1.8.5, libgpg-error-1.36, libgsf-1.14.44, libiconv-1.14_11, libidn2-2.2.0, libinotify-20180201_1, libogg-1.3.4,4, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, librsvg2-2.40.20, libtasn1-4.14, libtheora-1.1.1_7, libunistring-0.9.10_1, libunwind-20170615, libv4l-1.6.3_4, libva-2.5.0, libvdpau-1.1.1_2, libvorbis-1.3.6,3, libvpx-1.8.1_1, libx264-0.157.2980, libxcb-1.13.1, libxkbcommon-0.8.4, libxml2-2.9.9, libxshmfence-1.3, libxslt-1.1.33, mesa-libs-18.3.2_1, mkfontscale-1.2.1, nettle-3.5.1_1, nspr-4.22, opencv-core-3.4.1_22, openjdk8-8.222.10.1_2, openjfx8-devel-8.u202.b07_2,1, opus-1.3.1, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, pixman-0.38.4, png-1.6.37, polkit-0.114_3, python36-3.6.9, readline-8.0.0, shared-mime-info-1.10_1, sndio-1.6.0, spidermonkey52-52.9.0_4, sqlite3-3.29.0, tiff-4.0.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, wayland-protocols-1.17, x265-3.1.2_2, xkeyboard-config-2.27, xorg-fonts-truetype-7.7_1, xorgproto-2019.1, xvid-1.3.5,1
Also listed in: Java

infernal-1.1.2
Search sequence databases for structural RNA homologs
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

io_lib-1.14.10
General purpose trace file (and Experiment File) reading interface
Long description | Changes | Main Web Site
Maintained by: danilo@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, ca_root_nss-3.46, curl-7.66.0, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libnghttp2-1.39.2, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.30.0

iqtree-1.6.12
Efficient phylogenomic software by maximum likelihood
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.32_1,1, ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, eigen-3.3.7, expat-2.2.6_1, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.0.2, ninja-1.9.0,2, python36-3.6.9, readline-8.0.0, rhash-1.3.5

jalview-2.07_2
Viewer and editor for multiple sequence alignments
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: alsa-lib-1.1.2_2, apache-ant-1.10.6, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, giflib-5.1.9, java-zoneinfo-2019.b, javavmwrapper-2.7.3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, mkfontscale-1.2.1, openjdk8-8.222.10.1_2, xorgproto-2019.1
Also listed in: Java

kallisto-0.46.0_1
Quantify abundances of transcripts from RNA-Seq data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, hdf-szip-2.1.1, hdf5-1.10.5_2, htslib-1.9, jsoncpp-1.8.1_7, libarchive-3.4.0,1, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, rhash-1.3.5

lagan-2.0_1
Efficient tools for large-scale multiple alignments of genomic DNA
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: perl5-5.30.0

lamarc-2.1.8_1
Package of programs for computing population parameters
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

libbigwig-0.4.4
C library for handling bigWig files (containing genomic data)
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.46, curl-7.66.0, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libnghttp2-1.39.2

libgtextutils-0.7
Gordon's text utilities
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, indexinfo-0.3.1, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.30.0, pkgconf-1.6.3,1

libsbml-5.18.0
API Library for Working with SBML File
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, gettext-runtime-0.20.1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, libxml2-2.9.9, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.9, readline-8.0.0, rhash-1.3.5
Also listed in: Devel

linux-foldingathome-5.04
Distributed client for Protein Folding
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: linux_base-c7-7.6.1810_7

mafft-7.266
Multiple alignment program for amino acid or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

mapm3-3.0
Constructs linkage maps of markers segregating in experimental crosses
Long description | Changes | Main Web Site
Maintained by: tphilipp@potion-studios.com

migrate-3.6.11
Program to estimate population sizes and migration rates
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

minc2-2.2.00_9
Medical Imaging NetCDF
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, bash-5.0.11, bison-3.4.1,1, ca_root_nss-3.46, curl-7.66.0, gettext-runtime-0.20.1, gmake-4.2.1_3, hdf-szip-2.1.1, hdf5-1.10.5_2, indexinfo-0.3.1, libnghttp2-1.39.2, libtextstyle-0.20.1, libtool-2.4.6_1, m4-1.4.18_1,1, netcdf-4.7.1, perl5-5.30.0, pkgconf-1.6.3,1
Also listed in: Science

minimap2-2.17
Pairwise aligner for genomic and spliced nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

mmtf-cpp-1.0.0_2
C++ MMTF format API, decoder and encoder, for molecular structures
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, gettext-runtime-0.20.1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, msgpack-3.2.0_1, ninja-1.9.0,2, python36-3.6.9, readline-8.0.0, rhash-1.3.5
Also listed in: Science

molden-5.8.2_3
Display molecular orbitals and electron densities in 2D and 3D
Long description | Changes | Main Web Site
Maintained by: jmd@FreeBSD.org
Requires: binutils-2.32_1,1, expat-2.2.6_1, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, libGLU-9.0.0_3, libX11-1.6.8,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXxf86vm-1.1.4_3, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, mpc-1.1.0_2, mpfr-4.0.2, pciids-20190725, wayland-1.16.0_1, xorgproto-2019.1

mopac-7.1.15_8
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.32_1,1, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2

mothur-1.42.3_1
Software for bioinformatics of the microbial ecology community
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: bash-5.0.11, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, readline-8.0.0

mrbayes-3.1.2_3
Bayesian inference of phylogeny
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, readline-8.0.0

mummer-4.0.0.b2.2_2
Modular system for rapid whole genome alignment
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libedit-3.1.20190324,1, libffi-3.2.1_3, libtool-2.4.6_1, libunwind-20170615, libyaml-0.2.2, m4-1.4.18_1,1, perl5-5.30.0, ruby-2.6.4,1, yaggo-1.5.9

muscle-3.8.31
MUltiple Sequence Comparison by Log-Expectation
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp

ncbi-blast-2.9.0_3
NCBI implementation of Basic Local Alignment Search Tool
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, ca_root_nss-3.46, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, gnutls-3.6.9, indexinfo-0.3.1, libffi-3.2.1_3, libgcrypt-1.8.5, libgpg-error-1.36, libidn2-2.2.0, libtasn1-4.14, libunistring-0.9.10_1, lmdb-0.9.24,1, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.5.1_1, p11-kit-0.23.17, p5-Exporter-Tiny-1.002001, p5-JSON-2.97.001, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, pcre-8.43_2, perl5-5.30.0, python36-3.6.9, readline-8.0.0, sqlite3-3.29.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2
Also listed in: Perl5, Python

ncbi-cxx-toolkit-21.0.0_2
NCBI C++ Toolkit
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: bash-5.0.11, ca_root_nss-3.46, curl-7.66.0, cyrus-sasl-2.1.27, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXpm-3.5.12_2, libXt-1.2.0,1, libedit-3.1.20190324,1, libevent-2.1.11, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, mysql57-client-5.7.27, pcre-8.43_2, perl5-5.30.0, protobuf-3.9.1,1, python36-3.6.9, readline-8.0.0, xorgproto-2019.1
Also listed in: Science, Devel

ncbi-toolkit-2017.01.06_3
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.46, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, gettext-runtime-0.20.1, gmp-6.1.2_1, gnutls-3.6.9, indexinfo-0.3.1, jpeg-turbo-2.0.2, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXaw-1.0.13_2,2, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.2_3, libXmu-1.1.3,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXrender-0.9.10_2, libXt-1.2.0,1, libffi-3.2.1_3, libidn2-2.2.0, libpthread-stubs-0.4, libtasn1-4.14, libunistring-0.9.10_1, libxcb-1.13.1, libxml2-2.9.9, nettle-3.5.1_1, open-motif-2.3.8, p11-kit-0.23.17, png-1.6.37, tpm-emulator-0.7.4_2, trousers-0.3.14_2, xbitmaps-1.1.2, xorgproto-2019.1

nest-2.18.0_1
Simulator for spiking neural network models
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, gettext-runtime-0.20.1, gsl-2.5_1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libffi-3.2.1_3, libltdl-2.4.6, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, ninja-1.9.0,2, openmp-8.0.0_2, pkgconf-1.6.3,1, py35-setuptools-41.2.0, py36-cython-0.29_1, python35-3.5.7_2, python36-3.6.9, readline-8.0.0, rhash-1.3.5
Also listed in: Science

ngs-sdk-2.10.0
Tools and libraries for using data in the INSDC Sequence Read Archives
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, perl5-5.30.0

p5-AcePerl-1.92_5
Perl5 interface to the ACEDB genome database system
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Cache-2.11, p5-Cache-Cache-1.08, p5-Digest-SHA1-2.13_1, p5-Error-0.17028, p5-File-NFSLock-1.29, p5-Heap-0.80_1, p5-IO-String-1.08_1, p5-IPC-ShareLite-0.17_1, p5-TimeDate-2.30_2,1, perl5-5.30.0
Also listed in: Databases, Perl5

p5-Bio-ASN1-EntrezGene-1.73
Regular expression-based Perl Parser for NCBI Entrez Gene
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: expat-2.2.6_1, libiconv-1.14_11, libxml2-2.9.9, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007006, p5-Class-Data-Inheritable-0.08_1, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17028, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4229, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.128, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0134,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.29, p5-libwww-6.39, p5-libxml-0.08_1, perl5-5.30.0
Also listed in: Perl5

p5-Bio-Cluster-1.7.3
BioPerl cluster modules
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.6_1, libiconv-1.14_11, libxml2-2.9.9, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007006, p5-Class-Data-Inheritable-0.08_1, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17028, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4229, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.128, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0134,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.29, p5-libwww-6.39, p5-libxml-0.08_1, perl5-5.30.0
Also listed in: Perl5

p5-Bio-Coordinate-1.007001
Modules for working with biological coordinates
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.6_1, libiconv-1.14_11, libxml2-2.9.9, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007006, p5-Class-Data-Inheritable-0.08_1, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17028, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4229, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.128, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0134,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.29, p5-libwww-6.39, p5-libxml-0.08_1, perl5-5.30.0
Also listed in: Perl5

p5-Bio-Das-1.17_4
Client-side library for Distributed Genome Annotation System
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: expat-2.2.6_1, libiconv-1.14_11, libxml2-2.9.9, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007006, p5-Class-Data-Inheritable-0.08_1, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17028, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4229, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.128, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0134,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.29, p5-libwww-6.39, p5-libxml-0.08_1, perl5-5.30.0
Also listed in: Perl5

p5-Bio-Das-Lite-2.11_1
Perl extension for the DAS (HTTP+XML) Protocol
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: ca_root_nss-3.46, curl-7.66.0, libnghttp2-1.39.2, p5-Authen-NTLM-1.09_1, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-File-Listing-6.04_1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-LWP-MediaTypes-6.04, p5-Module-Build-0.4229, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-Readonly-2.05, p5-Socket6-0.29, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-Curl-4.17_2, p5-WWW-RobotRules-6.02_1, p5-libwww-6.39, perl5-5.30.0
Also listed in: Perl5

p5-Bio-FeatureIO-1.6.905
Handler for FeatureIO
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.6_1, libiconv-1.14_11, libxml2-2.9.9, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007006, p5-Class-Data-Inheritable-0.08_1, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17028, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4229, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.128, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0134,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.29, p5-libwww-6.39, p5-libxml-0.08_1, perl5-5.30.0
Also listed in: Perl5

p5-Bio-GFF3-2.0_2
Fast low-level functions for parsing and formatting GFF3
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Exporter-Tiny-1.002001, p5-File-ReadBackwards-1.05_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-URI-1.76, perl5-5.30.0
Also listed in: Perl5

p5-Bio-Glite-0.10_2
Perl Interface to G-language
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Authen-NTLM-1.09_1, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-File-Listing-6.04_1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-LWP-MediaTypes-6.04, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-Socket6-0.29, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-libwww-6.39, perl5-5.30.0
Also listed in: Perl5

p5-Bio-Graphics-2.40_2
Generate GD Images of Bio::Seq Objects
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: ca_root_nss-3.46, curl-7.66.0, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, giflib-5.1.9, io_lib-1.14.10, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libnghttp2-1.39.2, libxml2-2.9.9, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Bio-Coordinate-1.007001, p5-Bio-SCF-1.03_2, p5-BioPerl-1.007006, p5-CGI-4.44, p5-Class-Data-Inheritable-0.08_1, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17028, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-GD-2.71, p5-GD-SVG-0.33_6, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4229, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-SVG-2.84, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Statistics-Descriptive-3.0702, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.128, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0134,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.29, p5-libwww-6.39, p5-libxml-0.08_1, perl5-5.30.0, png-1.6.37, tiff-4.0.10_1, webp-1.0.3_1
Also listed in: Perl5

p5-Bio-MAGETAB-1.31_2
Data model and utility API for the MAGE-TAB format
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Algorithm-C3-0.10_1, p5-B-Hooks-EndOfScope-0.24, p5-Carp-Clan-6.07, p5-Class-C3-0.34, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.36, p5-Class-Load-0.25, p5-Class-Load-XS-0.10, p5-Class-Method-Modifiers-2.13, p5-Class-Singleton-1.5_1, p5-Data-OptList-0.110, p5-Date-Manip-6.78, p5-DateTime-1.51, p5-DateTime-Format-DateManip-0.04_1, p5-DateTime-Locale-1.24, p5-DateTime-TimeZone-2.36,1, p5-Devel-GlobalDestruction-0.14, p5-Devel-OverloadInfo-0.005, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Dist-CheckConflicts-0.11_1, p5-Email-Valid-1.202, p5-Eval-Closure-0.14, p5-Exception-Class-1.44, p5-File-ShareDir-1.116, p5-MRO-Compat-0.13, p5-Mail-Tools-2.19, p5-Module-Implementation-0.09_1, p5-Module-Runtime-0.016, p5-Module-Runtime-Conflicts-0.003_1, p5-Moose-2.2011,1, p5-MooseX-FollowPBP-0.05_1, p5-MooseX-Types-0.50, p5-Net-DNS-1.21,1, p5-Net-Domain-TLD-1.74, p5-Package-DeprecationManager-0.17_1, p5-Package-Stash-0.38, p5-Package-Stash-XS-0.29, p5-Params-Coerce-0.14_2, p5-Params-Util-1.07_2, p5-Params-Validate-1.29, p5-Params-ValidationCompiler-0.30_1, p5-Parse-RecDescent-1.967015, p5-Role-Tiny-2.000008, p5-Scalar-List-Utils-1.52,1, p5-Specio-0.44, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-ForMethods-0.100052, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Identify-0.14, p5-Sub-Install-0.928_1, p5-Sub-Name-0.21,1, p5-Sub-Quote-2.006003, p5-Text-CSV_XS-1.34, p5-TimeDate-2.30_2,1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-Variable-Magic-0.62, p5-namespace-autoclean-0.29, p5-namespace-clean-0.27, perl5-5.30.0
Also listed in: Perl5

p5-Bio-NEXUS-0.78_1
Object-oriented Perl API for the NEXUS file format
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: p5-Clone-PP-1.07, perl5-5.30.0
Also listed in: Perl5

p5-Bio-Phylo-2.0.1
Phylogenetic analysis using Perl
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, giflib-5.1.9, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libxml2-2.9.9, p5-Algorithm-C3-0.10_1, p5-Algorithm-Combinatorics-0.27_1, p5-Algorithm-Diff-1.1903, p5-Archive-Zip-1.65, p5-Authen-NTLM-1.09_1, p5-B-Hooks-EndOfScope-0.24, p5-B-Hooks-OP-Check-0.22, p5-BioPerl-1.007006, p5-Cache-LRU-0.04_1, p5-Class-C3-0.34, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.36, p5-Class-Load-0.25, p5-Class-Load-XS-0.10, p5-Class-Method-Modifiers-2.13, p5-Class-Singleton-1.5_1, p5-DBD-SQLite-1.64, p5-DBI-1.642, p5-DBIx-Connector-0.56, p5-Data-OptList-0.110, p5-Data-Perl-0.002009_1, p5-Data-Stag-0.14_2, p5-Data-TemporaryBag-0.09_1, p5-Data-UUID-1.224, p5-DateTime-1.51, p5-DateTime-Format-W3CDTF-0.07, p5-DateTime-Locale-1.24, p5-DateTime-TimeZone-2.36,1, p5-Devel-GlobalDestruction-0.14, p5-Devel-OverloadInfo-0.005, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Dist-CheckConflicts-0.11_1, p5-Encode-Locale-1.05, p5-Error-0.17028, p5-Eval-Closure-0.14, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-File-ShareDir-1.116, p5-Font-TTF-1.06, p5-GD-2.71, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-Hash-FieldHash-0.15, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-IRI-0.009, p5-JSON-2.97.001, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Log-Log4perl-1.49, p5-MRO-Compat-0.13, p5-Math-Bezier-Convert-0.02_1, p5-Math-CDF-0.1_2, p5-Math-Random-0.72, p5-Module-Build-0.4229, p5-Module-Implementation-0.09_1, p5-Module-Pluggable-5.2, p5-Module-Runtime-0.016, p5-Module-Runtime-Conflicts-0.003_1, p5-Moo-2.003004, p5-MooX-HandlesVia-0.001008, p5-Moose-2.2011,1, p5-MooseX-ArrayRef-0.005, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-PDF-API2-2.035, p5-Package-DeprecationManager-0.17_1, p5-Package-Stash-0.38, p5-Package-Stash-XS-0.29, p5-Params-Util-1.07_2, p5-Params-Validate-1.29, p5-Params-ValidationCompiler-0.30_1, p5-Parse-RecDescent-1.967015, p5-RDF-Query-2.918, p5-RDF-Trine-1.019_1, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.000008, p5-SVG-2.84, p5-SWF-Builder-0.16_2, p5-SWF-File-0.42_2,1, p5-Scalar-List-Utils-1.52,1, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Specio-0.44, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Identify-0.14, p5-Sub-Install-0.928_1, p5-Sub-Name-0.21,1, p5-Sub-Quote-2.006003, p5-Sub-Uplevel-0.2800, p5-Term-ANSIColor-4.06, p5-Test-Deep-1.128, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Aligner-0.13, p5-Text-CSV_XS-1.34, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Text-Table-1.133, p5-Tie-IxHash-1.23_1, p5-Try-Tiny-0.30, p5-Type-Tie-0.014, p5-Type-Tiny-1.004004, p5-Type-Tiny-XS-0.016, p5-URI-1.76, p5-Variable-Magic-0.62, p5-WWW-RobotRules-6.02_1, p5-XML-CommonNS-0.06_2, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0134,1, p5-XML-Namespace-0.02_1, p5-XML-NamespaceFactory-1.02, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XML2JSON-0.06_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.29, p5-YAML-Syck-1.31, p5-bareword-filehandles-0.007, p5-indirect-0.33, p5-libwww-6.39, p5-libxml-0.08_1, p5-multidimensional-0.014, p5-namespace-autoclean-0.29, p5-namespace-clean-0.27, p5-strictures-2.000006,1, perl5-5.30.0, png-1.6.37, tiff-4.0.10_1, webp-1.0.3_1
Also listed in: Perl5

p5-Bio-SCF-1.03_2
Read and Update SCF Chromatographic Sequence Files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: ca_root_nss-3.46, curl-7.66.0, io_lib-1.14.10, libnghttp2-1.39.2, perl5-5.30.0
Also listed in: Perl5

p5-BioPerl-1.007006
Collection of Perl modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.6_1, libiconv-1.14_11, libxml2-2.9.9, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Class-Data-Inheritable-0.08_1, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17028, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4229, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.128, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0134,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Writer-0.57, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.29, p5-libwww-6.39, p5-libxml-0.08_1, perl5-5.30.0
Also listed in: Perl5

p5-BioPerl-Run-1.007003
Wrapper modules for common bioinformatics tools
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.6_1, libiconv-1.14_11, libxml2-2.9.9, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Bio-Cluster-1.7.3, p5-Bio-FeatureIO-1.6.905, p5-BioPerl-1.007006, p5-Class-Data-Inheritable-0.08_1, p5-Config-Any-0.32, p5-Config-General-2.63, p5-Config-Tiny-2.24, p5-Cpanel-JSON-XS-4.12, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.04, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17028, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-File-Sort-1.01_1, p5-Graph-0.9704,1, p5-HTML-Parser-3.72, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.06, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.18, p5-HTTP-Negotiate-6.01_1, p5-Heap-0.80_1, p5-IO-HTML-1.001_1, p5-IO-Socket-INET6-2.72_1, p5-IO-Socket-SSL-2.066, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-LWP-MediaTypes-6.04, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Module-Build-0.4229, p5-Module-Pluggable-5.2, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.19, p5-Net-SSLeay-1.85, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Sub-Uplevel-0.2800, p5-Test-Deep-1.128, p5-Test-Differences-0.650,1, p5-Test-Exception-0.43, p5-Test-Most-0.35, p5-Test-RequiresInternet-0.05, p5-Test-Warn-0.36, p5-Text-Diff-1.45, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.30, p5-URI-1.76, p5-WWW-RobotRules-6.02_1, p5-XML-DOM-1.44_1, p5-XML-DOM-XPath-0.14_1, p5-XML-Filter-BufferText-1.01_1, p5-XML-LibXML-2.0134,1, p5-XML-NamespaceSupport-1.12, p5-XML-Parser-2.44, p5-XML-RegExp-0.04_1, p5-XML-SAX-1.02, p5-XML-SAX-Base-1.09, p5-XML-SAX-Expat-0.51_1, p5-XML-SAX-Writer-0.57, p5-XML-Simple-2.25, p5-XML-Twig-3.52, p5-XML-Writer-0.625_1, p5-XML-XPath-1.44, p5-XML-XPathEngine-0.14_1, p5-YAML-1.29, p5-YAML-LibYAML-0.80, p5-libwww-6.39, p5-libxml-0.08_1, perl5-5.30.0
Also listed in: Perl5

p5-TrimGalore-0.6.1
Wrapper around Cutadapt and FastQC for adapter and quality trimming
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: alsa-lib-1.1.2_2, dejavu-2.37_1, expat-2.2.6_1, fastqc-0.11.5, fontconfig-2.12.6,1, freetype2-2.10.1, gettext-runtime-0.20.1, giflib-5.1.9, indexinfo-0.3.1, java-zoneinfo-2019.b, javavmwrapper-2.7.3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libffi-3.2.1_3, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, mkfontscale-1.2.1, openjdk8-8.222.10.1_2, perl5-5.30.0, pigz-2.4, py35-setuptools-41.2.0, py36-bz2file-0.98, py36-cutadapt-2.5, py36-dnaio-0.3, py36-xopen-0.8.2, python35-3.5.7_2, python36-3.6.9, readline-8.0.0, xorgproto-2019.1, zopfli-1.0.2
Also listed in: Perl5, Python

p5-transdecoder-5.4.0_2
Identify candidate coding regions within transcript sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, cd-hit-4.8.1_1, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2, p5-URI-1.76, perl5-5.30.0
Also listed in: Perl5

paml-4.9i
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

pbbam-0.18.0_3
PacBio BAM C++ library, with SWIG bindings
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: boost-libs-1.71.0, ca_root_nss-3.46, curl-7.66.0, gettext-runtime-0.20.1, htslib-1.9, icu-64.2,1, indexinfo-0.3.1, libffi-3.2.1_3, libnghttp2-1.39.2, meson-0.51.2, ninja-1.9.0,2, pkgconf-1.6.3,1, py35-setuptools-41.2.0, python35-3.5.7_2, python36-3.6.9, readline-8.0.0

pbcopper-0.4.1_3
Core C++ library for Pacific Biosciences tools
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: boost-libs-1.71.0, gettext-runtime-0.20.1, icu-64.2,1, indexinfo-0.3.1, libffi-3.2.1_3, meson-0.51.2, ninja-1.9.0,2, py35-setuptools-41.2.0, python35-3.5.7_2, python36-3.6.9, readline-8.0.0

pbseqan-g20171011
Pacific Biosciences patched and stripped down SeqAn
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

pear-merger-0.9.6
Memory-efficient and highly accurate paired-end read merger
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

phrap-1.090518
Phrap is a program for assembling shotgun DNA sequence data
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp

phred-0.020425.c
Base calling and quality value assignment on DNA sequencing
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp

phylip-3.697
Phylogeny Inference Package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bash-5.0.11, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXaw-1.0.13_2,2, libXdmcp-1.1.3, libXext-1.3.4,1, libXmu-1.1.3,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXt-1.2.0,1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, xorgproto-2019.1

phyml-3.3.20190909
Simple, fast, and accurate algorithm to estimate large phylogenies
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, indexinfo-0.3.1, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.30.0, pkgconf-1.6.3,1

plinkseq-0.10_1
Toolset for working with human genetic variation data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1
Also listed in: Science

primer3-2.3.6
Primer3 helps to choose primers for PCR reactions
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

prodigal-2.6.3.2
Protein-coding gene prediction for prokaryotic genomes
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

prodigy-lig-1.0.0.3_1
Prediction of protein-small molecule binding affinities
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: adobe-cmaps-20051217_4, binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, gcc9-9.2.0, gettext-runtime-0.20.1, giflib-5.1.9, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_8, lcms2-2.9, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.2_3, libXrender-0.9.10_2, libffi-3.2.1_3, libfontenc-1.1.4, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, openjpeg-2.3.1, png-1.6.37, py27-biopython-1.73_1, py35-setuptools-41.2.0, py36-olefile-0.46, py36-pillow-6.1.0, py36-reportlab-3.5.21, py36-tkinter-3.6.9_6, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, webp-1.0.3_1, xorgproto-2019.1
Also listed in: Python

protomol-2.0.3_14
OO, component based, framework for molecular dynamics (MD) simulations
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: expat-2.2.6_1, freeglut-3.0.0_2, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libGLU-9.0.0_3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, pciids-20190725, png-1.6.37, tiff-4.0.10_1, wayland-1.16.0_1, xorgproto-2019.1

psi88-1.0_16
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.32_1,1, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2

py27-Genesis-PyAPI-1.2.1
API for the Genesis platform for genetics information processing
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py27-asn1crypto-0.24.0, py27-certifi-2019.6.16, py27-chardet-3.0.4_1, py27-idna-2.8, py27-ipaddress-1.0.22, py27-openssl-19.0.0, py27-pycparser-2.19, py27-pysocks-1.7.0, py27-urllib3-1.22,1, py35-setuptools-41.2.0, py36-cffi-1.12.3, py36-cryptography-2.6.1, py36-requests-2.21.0, py36-six-1.12.0, py36-slumber-0.7.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py27-biom-format-2.1.7_3
Biological Observation Matrix (BIOM) Format Project
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, hdf-szip-2.1.1, hdf5-1.10.5_2, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, perl5-5.30.0, postgresql11-client-11.5, py27-click-7.0, py27-dateutil-2.8.0, py27-pandas-0.24.2_1,1, py27-pyqi-0.3.2_2, py27-scipy-1.2.2_1, py35-setuptools-41.2.0, py36-bottleneck-1.2.1_5, py36-future-0.17.1_1, py36-h5py-2.10.0, py36-numexpr-2.7.0, py36-pytz-2019.2,1, py36-six-1.12.0, py37-numpy-1.16.5,1, py37-sqlite3-3.7.4_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, sqlite3-3.29.0, suitesparse-5.2.0_4
Also listed in: Python

py27-biopython-1.73_1
Collection of Python modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: adobe-cmaps-20051217_4, binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, gcc9-9.2.0, gettext-runtime-0.20.1, giflib-5.1.9, gmp-6.1.2_1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_8, lcms2-2.9, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.2_3, libXrender-0.9.10_2, libffi-3.2.1_3, libfontenc-1.1.4, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, openjpeg-2.3.1, png-1.6.37, py35-setuptools-41.2.0, py36-olefile-0.46, py36-pillow-6.1.0, py36-reportlab-3.5.21, py36-tkinter-3.6.9_6, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, webp-1.0.3_1, xorgproto-2019.1
Also listed in: Python

py27-bx-python-0.8.4_1
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, lzo2-2.10_1, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py27-python-lzo-1.12, py35-setuptools-41.2.0, py36-cython-0.29_1, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4
Also listed in: Python

py27-chainer-chemistry-0.5.0
Library for deep learning in biology and chemistry
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: atk-2.28.1, avahi-app-0.7_2, binutils-2.32_1,1, blas-3.5.0_6, ca_root_nss-3.46, cairo-1.16.0,2, cblas-1.0_12, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gcc9-9.2.0, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_8, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libglade2-2.6.4_9, libiconv-1.14_11, libidn2-2.2.0, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.5.1_1, openblas-0.2.20_10,1, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, pixman-0.38.4, png-1.6.37, protobuf-3.9.1,1, py27-backports-1, py27-backports.functools_lru_cache-1.5, py27-dateutil-2.8.0, py27-filelock-3.0.12, py27-gobject-2.28.6_8, py27-gtk2-2.24.0_5, py27-joblib-0.13.0, py27-kiwisolver-1.1.0, py27-matplotlib-2.2.4_1, py27-pandas-0.24.2_1,1, py27-scipy-1.2.2_1, py35-setuptools-41.2.0, py36-bottleneck-1.2.1_5, py36-cairo-1.18.1_1, py36-chainer-6.3.0, py36-cycler-0.10.0, py36-numexpr-2.7.0, py36-pyparsing-2.4.1.1, py36-pytz-2019.2,1, py36-scikit-learn-0.20.3_1, py36-six-1.12.0, py36-tkinter-3.6.9_6, py36-tornado-5.1.1, py36-tqdm-4.35.0, py36-typing-extensions-3.7.4, py37-numpy-1.16.5,1, py37-sqlite3-3.7.4_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, shared-mime-info-1.10_1, sqlite3-3.29.0, suitesparse-5.2.0_4, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xmlcatmgr-2.2_2, xorg-fonts-truetype-7.7_1, xorgproto-2019.1
Also listed in: Science

py27-gffutils-0.9_1
Work with GFF and GTF files in a flexible database framework
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py27-simplejson-3.16.1, py35-setuptools-41.2.0, py36-argcomplete-1.10.0, py36-argh-0.26.2, py36-pyfaidx-0.5.5.2_1, py36-six-1.12.0, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py27-gtfparse-1.2.0_2
Parsing tools for GTF (gene transfer format) files
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py27-dateutil-2.8.0, py27-pandas-0.24.2_1,1, py35-setuptools-41.2.0, py36-bottleneck-1.2.1_5, py36-numexpr-2.7.0, py36-pytz-2019.2,1, py36-six-1.12.0, py37-numpy-1.16.5,1, py37-sqlite3-3.7.4_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, sqlite3-3.29.0, suitesparse-5.2.0_4
Also listed in: Python

py27-macs2-2.1.0.p20170505_3
Analysis of chromatin immunoprecipitation (ChIP) sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py35-setuptools-41.2.0, py36-cython-0.29_1, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4
Also listed in: Python

py27-pyfaidx-0.5.5.2_1
Efficient pythonic random access to fasta subsequences
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.2.0, py36-six-1.12.0, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py27-pyfasta-0.5.2_4
Fast, memory-efficient, pythonic access to fasta sequence files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py35-setuptools-41.2.0, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4
Also listed in: Python

py27-pymol-2.3.0_1
OpenGL-based molecular visualization system
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: avahi-app-0.7_2, binutils-2.32_1,1, blas-3.5.0_6, blt-2.5.3_3, ca_root_nss-3.46, cblas-1.0_12, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, etc_os-release-0.1_2, expat-2.2.6_1, fontconfig-2.12.6,1, freeglut-3.0.0_2, freetype2-2.10.1, gcc9-9.2.0, gdbm-1.18.1_1, gettext-runtime-0.20.1, giflib-5.1.9, glew-2.1.0, glib-2.56.3_6,1, glm-0.9.8.5_4,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, icu-64.2,1, indexinfo-0.3.1, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_8, lcms-1.19_6,1, libGLU-9.0.0_3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libiconv-1.14_11, libidn2-2.2.0, libmng-1.0.10_3, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxkbcommon-0.8.4, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, metis-5.1.0_8, mmtf-cpp-1.0.0_2, mpc-1.1.0_2, mpfr-4.0.2, msgpack-3.2.0_1, nettle-3.5.1_1, openblas-0.2.20_10,1, p11-kit-0.23.17, pciids-20190725, pcre-8.43_2, pcre2-10.33, png-1.6.37, py27-Pmw-2.0.1, py27-enum34-1.1.6, py27-msgpack-0.6.1, py27-qt5-core-5.12.2, py27-qt5-gui-5.12.2, py27-qt5-widgets-5.12.2, py35-setuptools-41.2.0, py36-qt5-opengl-5.12.2, py36-sip-4.19.17,1, py36-tkinter-3.6.9_6, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, qscintilla2-qt5-2.11.1_1, qt5-core-5.12.2_2, qt5-dbus-5.12.2_1, qt5-gui-5.12.2_1, qt5-imageformats-5.12.2_1, qt5-network-5.12.2_2, qt5-opengl-5.12.2_1, qt5-printsupport-5.12.2_1, qt5-widgets-5.12.2_1, qtchooser-66, readline-8.0.0, suitesparse-5.2.0_4, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.3_1, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.3_1, xkeyboard-config-2.27, xorgproto-2019.1, xprop-1.2.4, xset-1.2.4_3
Also listed in: Science, Python

py27-pysam-0.15.3
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.2.0, py36-cython-0.29_1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py27-python-nexus-1.63
Generic nexus file format reader for python
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.2.0, python27-2.7.16_1, python35-3.5.7_2, readline-8.0.0
Also listed in: Python

py27-xenaPython-1.0.10
API for Xena Hub to access genetic information shared through the hub
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.2.0, python27-2.7.16_1, python35-3.5.7_2, readline-8.0.0
Also listed in: Python

py36-Genesis-PyAPI-1.2.1
API for the Genesis platform for genetics information processing
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py27-asn1crypto-0.24.0, py27-certifi-2019.6.16, py27-chardet-3.0.4_1, py27-idna-2.8, py27-ipaddress-1.0.22, py27-openssl-19.0.0, py27-pycparser-2.19, py27-pysocks-1.7.0, py27-urllib3-1.22,1, py35-setuptools-41.2.0, py36-cffi-1.12.3, py36-cryptography-2.6.1, py36-requests-2.21.0, py36-six-1.12.0, py36-slumber-0.7.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py36-biom-format-2.1.7_3
Biological Observation Matrix (BIOM) Format Project
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, hdf-szip-2.1.1, hdf5-1.10.5_2, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py27-click-7.0, py27-dateutil-2.8.0, py27-pandas-0.24.2_1,1, py27-scipy-1.2.2_1, py35-setuptools-41.2.0, py36-bottleneck-1.2.1_5, py36-future-0.17.1_1, py36-h5py-2.10.0, py36-numexpr-2.7.0, py36-pytz-2019.2,1, py36-six-1.12.0, py37-numpy-1.16.5,1, py37-sqlite3-3.7.4_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, sqlite3-3.29.0, suitesparse-5.2.0_4
Also listed in: Python

py36-biopython-1.73_1
Collection of Python modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: adobe-cmaps-20051217_4, binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, gcc9-9.2.0, gettext-runtime-0.20.1, giflib-5.1.9, gmp-6.1.2_1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_8, lcms2-2.9, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXft-2.3.2_3, libXrender-0.9.10_2, libffi-3.2.1_3, libfontenc-1.1.4, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, openjpeg-2.3.1, png-1.6.37, py35-setuptools-41.2.0, py36-olefile-0.46, py36-pillow-6.1.0, py36-reportlab-3.5.21, py36-tkinter-3.6.9_6, py37-numpy-1.16.5,1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, webp-1.0.3_1, xorgproto-2019.1
Also listed in: Python

py36-bx-python-0.8.4_1
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, lzo2-2.10_1, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py27-python-lzo-1.12, py35-setuptools-41.2.0, py36-cython-0.29_1, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4
Also listed in: Python

py36-chainer-chemistry-0.5.0
Library for deep learning in biology and chemistry
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: atk-2.28.1, avahi-app-0.7_2, binutils-2.32_1,1, blas-3.5.0_6, ca_root_nss-3.46, cairo-1.16.0,2, cblas-1.0_12, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gcc9-9.2.0, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_8, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libglade2-2.6.4_9, libiconv-1.14_11, libidn2-2.2.0, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, metis-5.1.0_8, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.5.1_1, openblas-0.2.20_10,1, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, pixman-0.38.4, png-1.6.37, protobuf-3.9.1,1, py27-backports-1, py27-backports.functools_lru_cache-1.5, py27-dateutil-2.8.0, py27-filelock-3.0.12, py27-gobject-2.28.6_8, py27-gtk2-2.24.0_5, py27-joblib-0.13.0, py27-kiwisolver-1.1.0, py27-matplotlib-2.2.4_1, py27-pandas-0.24.2_1,1, py27-scipy-1.2.2_1, py35-setuptools-41.2.0, py36-bottleneck-1.2.1_5, py36-cairo-1.18.1_1, py36-chainer-6.3.0, py36-cycler-0.10.0, py36-numexpr-2.7.0, py36-pyparsing-2.4.1.1, py36-pytz-2019.2,1, py36-scikit-learn-0.20.3_1, py36-six-1.12.0, py36-tkinter-3.6.9_6, py36-tornado-5.1.1, py36-tqdm-4.35.0, py36-typing-extensions-3.7.4, py37-numpy-1.16.5,1, py37-sqlite3-3.7.4_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, shared-mime-info-1.10_1, sqlite3-3.29.0, suitesparse-5.2.0_4, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xmlcatmgr-2.2_2, xorg-fonts-truetype-7.7_1, xorgproto-2019.1
Also listed in: Science

py36-cutadapt-2.5
Trim adapters from high-throughput sequencing reads
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, pigz-2.4, py35-setuptools-41.2.0, py36-bz2file-0.98, py36-cython-0.29_1, py36-dnaio-0.3, py36-setuptools_scm-3.3.3, py36-xopen-0.8.2, python35-3.5.7_2, python36-3.6.9, readline-8.0.0, zopfli-1.0.2
Also listed in: Python

py36-deap-1.3.0_1
Distributed Evolutionary Algorithms in Python
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py35-setuptools-41.2.0, py37-numpy-1.16.5,1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4
Also listed in: Math, Science, Devel, Python

py36-dnaio-0.3
Read and write FASTQ and FASTA
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.2.0, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py36-fastTSNE-0.2.13_2
Fast, parallel implementations of t-SNE
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, fftw3-3.3.8_4, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libedit-3.1.20190324,1, libffi-3.2.1_3, libxml2-2.9.9, llvm60-6.0.1_7, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, openmp-8.0.0_2, perl5-5.30.0, py27-enum34-1.1.6, py27-llvmlite-0.25.0_3, py27-numba-0.40.1_5, py27-scipy-1.2.2_1, py27-singledispatch-3.4.0.3_1, py35-setuptools-41.2.0, py36-funcsigs-1.0.2, py36-scikit-learn-0.20.3_1, py36-six-1.12.0, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4, tbb-2019.5
Also listed in: Python

py36-gffutils-0.9_1
Work with GFF and GTF files in a flexible database framework
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py27-simplejson-3.16.1, py35-setuptools-41.2.0, py36-argcomplete-1.10.0, py36-argh-0.26.2, py36-pyfaidx-0.5.5.2_1, py36-six-1.12.0, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py36-gtfparse-1.2.0_2
Parsing tools for GTF (gene transfer format) files
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py27-dateutil-2.8.0, py27-pandas-0.24.2_1,1, py35-setuptools-41.2.0, py36-bottleneck-1.2.1_5, py36-numexpr-2.7.0, py36-pytz-2019.2,1, py36-six-1.12.0, py37-numpy-1.16.5,1, py37-sqlite3-3.7.4_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, sqlite3-3.29.0, suitesparse-5.2.0_4
Also listed in: Python

py36-loompy-2.0.17_1
Work with .loom files for single-cell RNA-seq data
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, hdf-szip-2.1.1, hdf5-1.10.5_2, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py27-dateutil-2.8.0, py27-pandas-0.24.2_1,1, py27-scipy-1.2.2_1, py35-setuptools-41.2.0, py36-bottleneck-1.2.1_5, py36-h5py-2.10.0, py36-numexpr-2.7.0, py36-pytz-2019.2,1, py36-six-1.12.0, py37-numpy-1.16.5,1, py37-sqlite3-3.7.4_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, sqlite3-3.29.0, suitesparse-5.2.0_4
Also listed in: Python

py36-orange3-bioinformatics-3.2.2_3
Orange add-on providing common functionality for bioinformatics
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, alsa-plugins-1.1.1_6, atk-2.28.1, avahi-app-0.7_2, binutils-2.32_1,1, blas-3.5.0_6, ca_root_nss-3.46, cairo-1.16.0,2, cblas-1.0_12, cups-2.2.12, dav1d-0.4.0, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, etc_os-release-0.1_2, expat-2.2.6_1, ffmpeg-4.2.1_1,1, fftw3-3.3.8_4, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freeglut-3.0.0_2, freetype2-2.10.1, fribidi-0.19.7, gcc9-9.2.0, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, giflib-5.1.9, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, graphviz-2.40.1_11, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, icu-64.2,1, indexinfo-0.3.1, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-2.0.2, jsoncpp-1.8.1_7, lapack-3.5.0_8, lcms-1.19_6,1, lcms2-2.9, libGLU-9.0.0_3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, 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xmlcatmgr-2.2_2, xorg-fonts-truetype-7.7_1, xorgproto-2019.1, xprop-1.2.4, xset-1.2.4_3, xvid-1.3.5,1
Also listed in: Python

py36-orange3-single-cell-0.8.2_3
Orange add-on for gene expression of single cell data
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, alsa-plugins-1.1.1_6, atk-2.28.1, avahi-app-0.7_2, binutils-2.32_1,1, blas-3.5.0_6, ca_root_nss-3.46, cairo-1.16.0,2, cblas-1.0_12, cups-2.2.12, dav1d-0.4.0, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, etc_os-release-0.1_2, expat-2.2.6_1, ffmpeg-4.2.1_1,1, fftw3-3.3.8_4, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freeglut-3.0.0_2, freetype2-2.10.1, fribidi-0.19.7, gcc9-9.2.0, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, giflib-5.1.9, glib-2.56.3_6,1, gmake-4.2.1_3, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, graphviz-2.40.1_11, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hdf-szip-2.1.1, hdf5-1.10.5_2, hicolor-icon-theme-0.17, icu-64.2,1, indexinfo-0.3.1, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-2.0.2, jsoncpp-1.8.1_7, lapack-3.5.0_8, lcms-1.19_6,1, lcms2-2.9, libGLU-9.0.0_3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_2,2, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXmu-1.1.3,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libedit-3.1.20190324,1, libepoll-shim-0.0.20190311, libevent-2.1.11, libffi-3.2.1_3, libfontenc-1.1.4, libgcrypt-1.8.5, libgd-2.2.5_1,1, libglade2-2.6.4_9, libgpg-error-1.36, libiconv-1.14_11, libidn2-2.2.0, libltdl-2.4.6, libmng-1.0.10_3, libogg-1.3.4,4, libpaper-1.1.24.4, libpci-3.6.2, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libtheora-1.1.1_7, libunistring-0.9.10_1, libunwind-20170615, libv4l-1.6.3_4, libva-2.5.0, libvdpau-1.1.1_2, libvorbis-1.3.6,3, libvpx-1.8.1_1, libx264-0.157.2980, libxcb-1.13.1, libxkbcommon-0.8.4, libxml2-2.9.9, 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qt5-webengine-5.12.2_3, qt5-widgets-5.12.2_1, qt5-xml-5.12.2_1, qt5-xmlpatterns-5.12.2_1, qtchooser-66, re2-20190701_1, readline-8.0.0, shared-mime-info-1.10_1, snappy-1.1.6_1, sqlite3-3.29.0, suitesparse-5.2.0_4, tbb-2019.5, tcl86-8.6.9_1, tiff-4.0.10_1, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.3_1, x265-3.1.2_2, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.3_1, xkeyboard-config-2.27, xmlcatmgr-2.2_2, xorg-fonts-truetype-7.7_1, xorgproto-2019.1, xprop-1.2.4, xset-1.2.4_3, xvid-1.3.5,1
Also listed in: Python

py36-pyfaidx-0.5.5.2_1
Efficient pythonic random access to fasta subsequences
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.2.0, py36-six-1.12.0, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py36-pyfasta-0.5.2_4
Fast, memory-efficient, pythonic access to fasta sequence files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py35-setuptools-41.2.0, py37-numpy-1.16.5,1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, suitesparse-5.2.0_4
Also listed in: Python

py36-pysam-0.15.3
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.2.0, py36-cython-0.29_1, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py36-python-nexus-1.63
Generic nexus file format reader for python
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.2.0, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

py36-xenaPython-1.0.10
API for Xena Hub to access genetic information shared through the hub
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.20.1, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.2.0, python35-3.5.7_2, python36-3.6.9, readline-8.0.0
Also listed in: Python

pycogent-1.9_3
Toolkit for statistical analysis of biological sequences
Long description | Changes | Main Web Site
Maintained by: python@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, ca_root_nss-3.46, cblas-1.0_12, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, libffi-3.2.1_3, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, py27-Babel-2.7.0, py27-MarkupSafe-1.1.1, py27-alabaster-0.7.6, py27-asn1crypto-0.24.0, py27-certifi-2019.6.16, py27-chardet-3.0.4_1, py27-docutils-0.15.2, py27-idna-2.8, py27-imagesize-1.1.0, py27-ipaddress-1.0.22, py27-openssl-19.0.0, py27-pycparser-2.19, py27-pysocks-1.7.0, py27-sphinx_rtd_theme-0.4.3, py27-urllib3-1.22,1, py35-setuptools-41.2.0, py36-Jinja2-2.10.1, py36-cffi-1.12.3, py36-cryptography-2.6.1, py36-cython-0.29_1, py36-pygments-2.4.1, py36-pystemmer-1.3.0_2, py36-pytz-2019.2,1, py36-requests-2.21.0, py36-six-1.12.0, py36-snowballstemmer-1.2.1, py36-sphinx-1.6.5_2,1, py36-sphinxcontrib-websupport-1.1.2, py36-sqlalchemy10-1.0.14, py37-numpy-1.16.5,1, py37-sqlite3-3.7.4_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, sqlite3-3.29.0, suitesparse-5.2.0_4
Also listed in: Python

rainbow-2.0.4
Efficient clustering and assembling of short reads, especially for RAD
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

raster3d-3.0.3_6
Set of tools for generating raster images of proteins and molecules
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ImageMagick6-6.9.10.57,1, avahi-app-0.7_2, binutils-2.32_1,1, ca_root_nss-3.46, cairo-1.16.0,2, cups-2.2.12, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, fftw3-3.3.8_4, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gcc9-9.2.0, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, ghostscript9-agpl-base-9.27_2, ghostscript9-agpl-x11-9.27, giflib-5.1.9, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gsfonts-8.11_8, harfbuzz-2.6.1_1, indexinfo-0.3.1, jbig2dec-0.16, jbigkit-2.1_1, jpeg-turbo-2.0.2, lcms2-2.9, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libcroco-0.6.12, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libgd-2.2.5_1,1, libgsf-1.14.44, libiconv-1.14_11, libidn-1.35, libidn2-2.2.0, liblqr-1-0.4.2, libltdl-2.4.6, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libraqm-0.6.0, libraw-0.19.2_1, librsvg2-2.40.20, libtasn1-4.14, libunistring-0.9.10_1, libunwind-20170615, libwmf-0.2.8.4_15, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.5.1_1, openjpeg-2.3.1, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, perl5-5.30.0, pixman-0.38.4, pkgconf-1.6.3,1, png-1.6.37, poppler-data-0.4.9, python36-3.6.9, readline-8.0.0, shared-mime-info-1.10_1, tiff-4.0.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.3_1, xorg-fonts-truetype-7.7_1, xorgproto-2019.1
Also listed in: Graphics

recombine-1.41_2
Program to fit population models across sites
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

rna-STAR-2.7.0.f_1
Spliced Transcripts Alignment to a Reference
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2

ruby26-bio-1.5.1
Integrated environment for Bioinformatics written in Ruby
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: indexinfo-0.3.1, libedit-3.1.20190324,1, libffi-3.2.1_3, libunwind-20170615, libyaml-0.2.2, ruby-2.6.4,1
Also listed in: Ruby

rubygem-bio-1.5.2
Integrated environment for Bioinformatics written in Ruby
Long description | Changes | Main Web Site
Maintained by: ruby@FreeBSD.org
Requires: indexinfo-0.3.1, libedit-3.1.20190324,1, libffi-3.2.1_3, libunwind-20170615, libyaml-0.2.2, ruby-2.6.4,1, ruby26-gems-3.0.6
Also listed in: Rubygems

samtools-1.9
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, ca_root_nss-3.46, curl-7.66.0, gettext-runtime-0.20.1, gmake-4.2.1_3, htslib-1.9, indexinfo-0.3.1, libnghttp2-1.39.2, m4-1.4.18_1,1, perl5-5.30.0

seaview-4.7
Multiple DNA/protein sequence alignment editor
Long description | Changes | Main Web Site
Maintained by: bofh@FreeBSD.org
Requires: expat-2.2.6_1, fltk-1.3.5, fontconfig-2.12.6,1, freetype2-2.10.1, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, jpeg-turbo-2.0.2, libGLU-9.0.0_3, libX11-1.6.8,1, libXau-1.0.9, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXinerama-1.1.4_2,1, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, pciids-20190725, png-1.6.37, wayland-1.16.0_1, xorgproto-2019.1

seqan-2.4.0
C++ sequence analysis template library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org

seqan-apps-2.4.0_8
Official bioinformatic applications based on the SeqAn library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: binutils-2.32_1,1, boost-libs-1.71.0, ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, icu-64.2,1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libarchive-3.4.0,1, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libuv-1.32.0, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.0.2, ninja-1.9.0,2, python36-3.6.9, readline-8.0.0, rhash-1.3.5

seqan1-1.3.1_4
C++ Sequence Analysis Library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org

seqio-1.2.2_1
Set of C functions which can read/write biological sequence files
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

seqtk-1.2.8
Tool for processing sequences in FASTA/FASTQ format
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

seqtools-4.44.1_4
Tools for visualising sequence alignments
Long description | Changes | Main Web Site
Maintained by: pi@FreeBSD.org
Requires: atk-2.28.1, avahi-app-0.7_2, ca_root_nss-3.46, cairo-1.16.0,2, cups-2.2.12, curl-7.66.0, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.5,1, expat-2.2.6_1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gdbm-1.18.1_1, gdk-pixbuf2-2.38.1, gettext-runtime-0.20.1, gettext-tools-0.20.1_1, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXcomposite-0.4.5,1, libXcursor-1.2.0, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXinerama-1.1.4_2,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libiconv-1.14_11, libidn2-2.2.0, libnghttp2-1.39.2, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libtextstyle-0.20.1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, mesa-libs-18.3.2_1, mkfontscale-1.2.1, nettle-3.5.1_1, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, pixman-0.38.4, pkgconf-1.6.3,1, png-1.6.37, python36-3.6.9, readline-8.0.0, shared-mime-info-1.10_1, sqlite3-3.29.0, tiff-4.0.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xorg-fonts-truetype-7.7_1, xorgproto-2019.1

sim4-2003.09.21_1
Algorithm for aligning expressed DNA with genomic sequences
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org

simbody-3.6.1_5
Multibody dynamics library for (bio)mechanical systems simulation
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, ca_root_nss-3.46, cmake-3.15.3, curl-7.66.0, expat-2.2.6_1, freeglut-3.0.0_2, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, jsoncpp-1.8.1_7, libGLU-9.0.0_3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXmu-1.1.3,1, libXrandr-1.5.2, libXrender-0.9.10_2, libXt-1.2.0,1, libXxf86vm-1.1.4_3, libarchive-3.4.0,1, libdrm-2.4.99,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, liblz4-1.9.2,1, libnghttp2-1.39.2, libpciaccess-0.16, libpthread-stubs-0.4, libunwind-20170615, libuv-1.32.0, libxcb-1.13.1, libxml2-2.9.9, libxshmfence-1.3, lzo2-2.10_1, mesa-libs-18.3.2_1, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_10,1, pciids-20190725, rhash-1.3.5, wayland-1.16.0_1, xorgproto-2019.1
Also listed in: Science

slclust-2010.02.02
Single-linkage clustering with Jaccard similarity
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

smithwaterman-g20160702
Smith-waterman-gotoh alignment algorithm
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

stacks-2.4_1
Software pipeline for building loci from short-read sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, libffi-3.2.1_3, mpc-1.1.0_2, mpfr-4.0.2, python36-3.6.9, readline-8.0.0
Also listed in: Perl5, Python

stringtie-1.3.4.d
Transcript assembly and quantification for RNA-seq
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1

tRNAscan-SE-2.0.3
Searching for tRNA genes in genomic sequence
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, indexinfo-0.3.1, infernal-1.1.2, m4-1.4.18_1,1, perl5-5.30.0

t_coffee-9.03_11
Multiple DNA or protein sequence alignment package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.32_1,1, clustalw-2.1_2, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2

tabixpp-1.0.0.10
C++ wrapper to tabix indexer
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.46, curl-7.66.0, htslib-1.9, libnghttp2-1.39.2

treekin-0.5.1_1
Efficient computation of RNA folding dynamics
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, gcc9-9.2.0, gettext-runtime-0.20.1, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_8, lapacke-3.5.0_8, mpc-1.1.0_2, mpfr-4.0.2

treepuzzle-5.2
Maximum likelihood phylogeny reconstruction using quartets
Long description | Changes | Main Web Site
Maintained by: jan.lentfer@web.de

trimadap-0.1.3
Trim adapter sequences from Illumina data using heuristic rules
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org

trimmomatic-0.39
Flexible read trimming tool for Illumina NGS data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: alsa-lib-1.1.2_2, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, giflib-5.1.9, java-zoneinfo-2019.b, javavmwrapper-2.7.3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXi-1.7.10,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.9, mkfontscale-1.2.1, openjdk8-8.222.10.1_2, xorgproto-2019.1
Also listed in: Java

ugene-1.31.0_1
Free, open-source, cross-platform bioinformatics toolkit
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: avahi-app-0.7_2, bash-5.0.11, brotli-1.0.7_2,1, ca_root_nss-3.46, cairo-1.16.0,2, cups-2.2.12, dav1d-0.4.0, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, desktop-file-utils-0.23, encodings-1.0.5,1, etc_os-release-0.1_2, expat-2.2.6_1, ffmpeg-4.2.1_1,1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, fontconfig-2.12.6,1, freetype2-2.10.1, fribidi-0.19.7, gdbm-1.18.1_1, gettext-runtime-0.20.1, giflib-5.1.9, glib-2.56.3_6,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.9, gobject-introspection-1.56.1,1, graphite2-1.3.13_1, gstreamer1-1.14.4, gstreamer1-libav-1.14.4_3, gstreamer1-plugins-1.14.4_2, gstreamer1-plugins-a52dec-1.14.4, gstreamer1-plugins-bad-1.14.4, gstreamer1-plugins-core-1.14, gstreamer1-plugins-dts-1.14.4, gstreamer1-plugins-dvdread-1.14.4, gstreamer1-plugins-good-1.14.4, gstreamer1-plugins-mpg123-1.14.4, gstreamer1-plugins-ogg-1.14.4, gstreamer1-plugins-pango-1.14.4, gstreamer1-plugins-png-1.14.4, gstreamer1-plugins-resindvd-1.14.4, gstreamer1-plugins-theora-1.14.4, gstreamer1-plugins-ugly-1.14.4, gstreamer1-plugins-vorbis-1.14.4, harfbuzz-2.6.1_1, hicolor-icon-theme-0.17, hyphen-2.8.8, icu-64.2,1, indexinfo-0.3.1, iso-codes-4.2, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-2.0.2, lcms-1.19_6,1, libGLU-9.0.0_3, libICE-1.0.10,1, libSM-1.2.3,1, libX11-1.6.8,1, libXau-1.0.9, libXcomposite-0.4.5,1, libXdamage-1.1.5, libXdmcp-1.1.3, libXext-1.3.4,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.10,1, libXmu-1.1.3,1, libXrender-0.9.10_2, libXt-1.2.0,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, liba52-0.7.4_3, libdaemon-0.14_1, libdca-0.0.6_1, libdrm-2.4.99,1, libdvdcss-1.4.2, libdvdnav-6.0.0, libdvdread-6.0.1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libgcrypt-1.8.5, libgpg-error-1.36, libiconv-1.14_11, libidn2-2.2.0, libmng-1.0.10_3, libogg-1.3.4,4, libpaper-1.1.24.4, libpciaccess-0.16, libpthread-stubs-0.4, libtasn1-4.14, libtheora-1.1.1_7, libunistring-0.9.10_1, libunwind-20170615, libv4l-1.6.3_4, libva-2.5.0, libvdpau-1.1.1_2, libvorbis-1.3.6,3, libvpx-1.8.1_1, libx264-0.157.2980, libxcb-1.13.1, libxkbcommon-0.8.4, libxml2-2.9.9, libxshmfence-1.3, libxslt-1.1.33, mesa-libs-18.3.2_1, mkfontscale-1.2.1, mpg123-1.25.12, nettle-3.5.1_1, opencv-core-3.4.1_22, opus-1.3.1, orc-0.4.28, p11-kit-0.23.17, pango-1.42.4_3, pciids-20190725, pcre-8.43_2, pcre2-10.33, perl5-5.30.0, pixman-0.38.4, png-1.6.37, python36-3.6.9, qt5-buildtools-5.12.2_1, qt5-concurrent-5.12.2_1, qt5-core-5.12.2_2, qt5-dbus-5.12.2_1, qt5-declarative-5.12.2_1, qt5-gui-5.12.2_1, qt5-imageformats-5.12.2_1, qt5-linguisttools-5.12.2_1, qt5-location-5.12.2_1, qt5-network-5.12.2_2, qt5-opengl-5.12.2_1, qt5-printsupport-5.12.2_1, qt5-qmake-5.12.2_2, qt5-script-5.12.2_1, qt5-scripttools-5.12.2_1, qt5-sensors-5.12.2_1, qt5-serialport-5.12.2_1, qt5-sql-5.12.2_1, qt5-svg-5.12.2_1, qt5-testlib-5.12.2_1, qt5-webchannel-5.12.2_1, qt5-webkit-5.212.0.a3_2, qt5-widgets-5.12.2_1, qt5-xml-5.12.2_1, qt5-xmlpatterns-5.12.2_1, qtchooser-66, readline-8.0.0, shared-mime-info-1.10_1, sqlite3-3.29.0, tiff-4.0.10_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.3_1, woff2-1.0.2_4, x265-3.1.2_2, xcb-util-0.4.0_2,1, xcb-util-image-0.4.0_1, xcb-util-keysyms-0.4.0_1, xcb-util-renderutil-0.3.9_1, xcb-util-wm-0.4.1_3, xdg-utils-1.1.3_1, xkeyboard-config-2.27, xorg-fonts-truetype-7.7_1, xorgproto-2019.1, xprop-1.2.4, xset-1.2.4_3, xvid-1.3.5,1
Also listed in: Science

unanimity-3.4.1_3
Pacific Biosciences consensus library and applications
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32_1,1, blas-3.5.0_6, boost-libs-1.71.0, ca_root_nss-3.46, cblas-1.0_12, curl-7.66.0, gcc9-9.2.0, gettext-runtime-0.20.1, gmp-6.1.2_1, htslib-1.9, icu-64.2,1, indexinfo-0.3.1, lapack-3.5.0_8, libedit-3.1.20190324,1, libffi-3.2.1_3, libnghttp2-1.39.2, lua52-5.2.4, meson-0.51.2, metis-5.1.0_8, mpc-1.1.0_2, mpfr-4.0.2, ninja-1.9.0,2, openblas-0.2.20_10,1, pbbam-0.18.0_3, pbcopper-0.4.1_3, pcre-8.43_2, pkgconf-1.6.3,1, py35-setuptools-41.2.0, py37-numpy-1.16.5,1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.9, python37-3.7.4, readline-8.0.0, seqan-2.4.0, suitesparse-5.2.0_4, swig30-3.0.12

vcflib-1.0.0.r1.130
C++ library and CLI tools for parsing and manipulating VCF files
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.46, curl-7.66.0, fastahack-g20160702, filevercmp-g20151117, fsom-g20151117_2, gettext-runtime-0.20.1, gmake-4.2.1_3, htslib-1.9, indexinfo-0.3.1, intervaltree-g20151213_2, libffi-3.2.1_3, libnghttp2-1.39.2, multichoose-1.0.3.2, python36-3.6.9, readline-8.0.0, smithwaterman-g20160702, tabixpp-1.0.0.10

vcftools-0.1.16
Tools for working with VCF genomics files
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, m4-1.4.18_1,1, perl5-5.30.0, pkgconf-1.6.3,1

velvet-1.2.10_2
Sequence assembler for very short reads
Long description | Changes | Main Web Site
Maintained by: mzaki@m.u-tokyo.ac.jp
Requires: gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, perl5-5.30.0, python36-3.6.9, readline-8.0.0

viennarna-2.4.13_1
Alignment tools for the structural analysis of RNA
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, bash-5.0.11, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.10.1, gettext-runtime-0.20.1, giflib-5.1.9, gmake-4.2.1_3, gmp-6.1.2_1, gsl-2.5_1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libX11-1.6.8,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.4,1, libgd-2.2.5_1,1, libpthread-stubs-0.4, libtool-2.4.6_1, libxcb-1.13.1, libxml2-2.9.9, m4-1.4.18_1,1, mpfr-4.0.2, perl5-5.30.0, pkgconf-1.6.3,1, png-1.6.37, tiff-4.0.10_1, webp-1.0.3_1, xorgproto-2019.1

vsearch-2.13.4
Versatile open-source tool for metagenomics
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_3, autoconf-wrapper-20131203, automake-1.16.1_2, gettext-runtime-0.20.1, gmake-4.2.1_3, indexinfo-0.3.1, libsysinfo-0.0.3_2, m4-1.4.18_1,1, perl5-5.30.0

wise-2.4.1_1
Intelligent algorithms for DNA searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.20.1, glib-2.56.3_6,1, indexinfo-0.3.1, libffi-3.2.1_3, libiconv-1.14_11, libxml2-2.9.9, pcre-8.43_2, pkgconf-1.6.3,1, python36-3.6.9, readline-8.0.0

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