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FreeBSD Ports: Biology

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Software related to biology.

CheckM-1.0.13_1
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, blas-3.5.0_5, ca_root_nss-3.44, cairo-1.16.0,2, cblas-1.0_11, cups-2.2.11, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.4_4,1, 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, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gcc8-8.3.0_2, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, glib-2.56.3_5,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.4.0_1, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_7, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libglade2-2.6.4_9, libiconv-1.14_11, libidn2-2.1.1, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, mesa-libs-18.3.2, metis-5.1.0_7, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.4.1_1, openblas-0.2.20_8,1, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, pixman-0.34.0_1, png-1.6.37, py27-backports-1, py27-backports.functools_lru_cache-1.5, py27-dateutil-2.7.3, py27-gobject-2.28.6_8, py27-gtk2-2.24.0_5, py27-kiwisolver-1.1.0, py27-matplotlib-2.2.4, py27-numpy-1.16.1_2,1, py27-pytz-2019.1,1, py27-six-1.12.0, py35-cython-0.29_1, py35-setuptools-41.0.0, py36-DendroPy-4.4.0, py36-cairo-1.14.1, py36-cycler-0.10.0, py36-pyparsing-2.4.0, py36-pysam-0.15.2, py36-scipy-1.2.0_1, py36-tkinter-3.6.8_6, py36-tornado-5.1.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, shared-mime-info-1.10_1, suitesparse-5.2.0_3, tcl86-8.6.9_1, tiff-4.0.10, 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-2018.4
Also listed in: Python

FastTree-2.1.10_3
Approximately-maximum-likelihood phylogenetic trees from alignments
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32,1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2

GroopM-0.3.4_1
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, blas-3.5.0_5, ca_root_nss-3.44, cairo-1.16.0,2, cblas-1.0_11, cups-2.2.11, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.4_4,1, 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, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gcc8-8.3.0_2, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, glib-2.56.3_5,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.4.0_1, hdf-szip-2.1.1, hdf5-1.10.5_1, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_7, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libglade2-2.6.4_9, libiconv-1.14_11, libidn2-2.1.1, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, lzo2-2.10_1, mesa-libs-18.3.2, metis-5.1.0_7, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.4.1_1, openblas-0.2.20_8,1, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, pixman-0.34.0_1, png-1.6.37, py27-backports-1, py27-backports.functools_lru_cache-1.5, py27-dateutil-2.7.3, py27-gobject-2.28.6_8, py27-gtk2-2.24.0_5, py27-kiwisolver-1.1.0, py27-matplotlib-2.2.4, py27-numexpr-2.6.9, py27-numpy-1.16.1_2,1, py27-pytz-2019.1,1, py27-six-1.12.0, py27-tables-3.5.1_2, py35-setuptools-41.0.0, py36-cairo-1.14.1, py36-cycler-0.10.0, py36-pyparsing-2.4.0, py36-scipy-1.2.0_1, py36-tkinter-3.6.8_6, py36-tornado-5.1.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, shared-mime-info-1.10_1, suitesparse-5.2.0_3, tcl86-8.6.9_1, tiff-4.0.10, 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-2018.4
Also listed in: Python

InsightToolkit-4.13.0_7
Insight Toolkit
Long description | Changes | Main Web Site
Maintained by: woodsb02@FreeBSD.org
Requires: binutils-2.32,1, ca_root_nss-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, fftw-2.1.5_21, gcc8-8.3.0_2, gdcm-2.8.9_1, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, googletest-1.8.1_2, hdf-szip-2.1.1, hdf5-1.10.5_1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, jsoncpp-1.8.1_6, lcms2-2.9, libarchive-3.3.3,1, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.0.2, ninja-1.9.0,2, openjpeg-2.3.1, png-1.6.37, python36-3.6.8_2, readline-8.0.0, rhash-1.3.5, tiff-4.0.10
Also listed in: Science

Jellyfish-2.2.10_5
Fast, memory-efficient counting of k-mers in DNA
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_2, autoconf-wrapper-20131203, automake-1.16.1_1, ca_root_nss-3.44, curl-7.64.1_1, gettext-runtime-0.19.8.1_2, gettext-tools-0.19.8.1_1, gmake-4.2.1_3, htslib-1.9, indexinfo-0.3.1, libedit-3.1.20181209_2,1, libffi-3.2.1_3, libnghttp2-1.38.0, libtool-2.4.6_1, libunwind-20170615, libyaml-0.2.2, m4-1.4.18_1,1, perl5-5.28.2, pkgconf-1.6.1,1, ruby-2.5.5_2,1, yaggo-1.5.9

abyss-2.1.5_2
Assembly By Short Sequences: parallel, paired-end sequence assembler
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: bash-5.0.7, boost-libs-1.70.0_2, gettext-runtime-0.19.8.1_2, ghc-8.6.3, gmake-4.2.1_3, gmp-6.1.2_1, hs-pandoc-2.7.1_1, icu-64.2,1, indexinfo-0.3.1, libffi-3.2.1_3, libiconv-1.14_11, openmp-8.0.0_1, readline-8.0.0, sqlite3-3.28.0

afni-2015.11.13_8
Advanced Functional Neuro Imaging
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: R-3.6.0_1, avahi-app-0.7_2, binutils-2.32,1, ca_root_nss-3.44, cairo-1.16.0,2, cups-2.2.11, curl-7.64.1_1, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.4_4,1, 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, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gcc8-8.3.0_2, gdbm-1.18.1_1, gettext-runtime-0.19.8.1_2, gettext-tools-0.19.8.1_1, ghostscript9-agpl-base-9.27_1, glib-2.56.3_5,1, gmake-4.2.1_3, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, gsl-2.5_1, harfbuzz-2.4.0_1, hdf-szip-2.1.1, hdf5-1.10.5_1, 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, libGLw-8.0.0_3, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_2,2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.9_2,1, libXmu-1.1.2_5,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libiconv-1.14_11, libidn-1.35, libidn2-2.1.1, libnghttp2-1.38.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, m4-1.4.18_1,1, mesa-libs-18.3.2, mkfontscale-1.2.1, mpc-1.1.0_2, mpeg_encode-1.5b, mpfr-4.0.2, netcdf-4.7.0, netcdf-fortran-4.4.5_2, netpbm-10.86.03, nettle-3.4.1_1, open-motif-2.3.8, openmp-8.0.0_1, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, perl5-5.28.2, pixman-0.34.0_1, pkgconf-1.6.1,1, png-1.6.37, poppler-data-0.4.9, python36-3.6.8_2, qhull5-1.0_3, readline-8.0.0, tcl86-8.6.9_1, tiff-4.0.10, 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-2018.4
Also listed in: Science, Graphics

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-5.0.7, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, gettext-runtime-0.19.8.1_2, giflib-5.1.8, gmake-4.2.1_3, indexinfo-0.3.1, java-zoneinfo-2019.a, javavmwrapper-2.6, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, mkfontscale-1.2.1, openjdk8-8.212.4.1, xorgproto-2018.4
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-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, gettext-runtime-0.19.8.1_2, indexinfo-0.3.1, jsoncpp-1.8.1_6, libarchive-3.3.3,1, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.8_2, 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-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, gettext-runtime-0.19.8.1_2, indexinfo-0.3.1, jsoncpp-1.8.1_6, libarchive-3.3.3,1, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.8_2, 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_2, autoconf-wrapper-20131203, automake-1.16.1_1, ca_root_nss-3.44, curl-7.64.1_1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, gsl-2.5_1, htslib-1.9, indexinfo-0.3.1, libnghttp2-1.38.0, m4-1.4.18_1,1, perl5-5.28.2

bedtools-2.27.1_2
Toolset for genome set arithmetic such as intersect, union
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, python36-3.6.8_2, 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-3.44, cairo-1.16.0,2, cups-2.2.11, dbus-1.12.12, dbus-glib-0.110, expat-2.2.6_1, flac-1.3.2, flite-2.1, fontconfig-2.12.6,1, freetype2-2.9.1, gdbm-1.18.1_1, gettext-runtime-0.19.8.1_2, giflib-5.1.8, glib-2.56.3_5,1, 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-3.6.7, gobject-introspection-1.56.1,1, icu-64.2,1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXmu-1.1.2_5,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXxf86vm-1.1.4_3, libao-1.2.0_4, libdaemon-0.14_1, libdrm-2.4.96,1, libedit-3.1.20181209_2,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libgcrypt-1.8.4_1, libgpg-error-1.36, libiconv-1.14_11, libidn2-2.1.1, libobjc2-2.0_1, libogg-1.3.3,4, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libsndfile-1.0.28_2, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libvorbis-1.3.6,3, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, libxslt-1.1.32, llvm70-7.0.1_3, mesa-libs-18.3.2, nettle-3.4.1_1, p11-kit-0.23.15, pciids-20190418, pcre-8.43_1, perl5-5.28.2, pixman-0.34.0_1, png-1.6.37, python27-2.7.16_1, python36-3.6.8_2, readline-8.0.0, tiff-4.0.10, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xorgproto-2018.4
Also listed in: Gnustep

bowtie-1.1.2_8
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32,1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, 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, perl5-5.28.2, python36-3.6.8_2, 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-5.0.7, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, perl5-5.28.2, python36-3.6.8_2, 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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, perl5-5.28.2

canu-1.8_3
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, boost-libs-1.70.0_2, ca_root_nss-3.44, cairo-1.16.0,2, cups-2.2.11, dbus-1.12.12, dbus-glib-0.110, dconf-0.28.0, dejavu-2.37_1, encodings-1.0.4_4,1, 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, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gcc8-8.3.0_2, gconf2-3.2.6_5, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, giflib-5.1.8, glib-2.56.3_5,1, gmake-4.2.1_3, gmp-6.1.2_1, gnome_subr-1.0, gnuplot-5.2.6_1, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, gstreamer-0.10.36_6, gstreamer-plugins-0.10.36_12,3, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.4.0_1, hicolor-icon-theme-0.17, icu-64.2,1, indexinfo-0.3.1, java-zoneinfo-2019.a, javavmwrapper-2.6, jbigkit-2.1_1, jpeg-turbo-2.0.2, libGLU-9.0.0_3, libICE-1.0.9_3,1, libIDL-0.8.14_4, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libXv-1.0.11_2,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libedit-3.1.20181209_2,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libgd-2.2.5_1,1, libiconv-1.14_11, libidn2-2.1.1, libinotify-20180201_1, libmspack-0.9.1, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, lua53-5.3.5_3, mesa-libs-18.3.2, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.4.1_1, nspr-4.21, openjdk8-8.212.4.1, orc-0.4.28, p11-kit-0.23.15, pango-1.42.4_2, pangox-compat-0.0.2_2, pciids-20190418, pcre-8.43_1, perl5-5.28.2, pixman-0.34.0_1, png-1.6.37, polkit-0.114_2, python36-3.6.8_2, readline-8.0.0, shared-mime-info-1.10_1, spidermonkey52-52.9.0_3, tex-kpathsea-6.2.1_2, tiff-4.0.10, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.2, wx28-gtk2-2.8.12_7, wx28-gtk2-common-2.8.12_7, xorg-fonts-truetype-7.7_1, xorgproto-2018.4
Also listed in: Java, Perl5

cd-hit-4.8.1
Clustering and comparing protein or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32,1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, 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-0.19.8.1_2, 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-3.3.2,1, gettext-runtime-0.19.8.1_2, indexinfo-0.3.1, 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-c6-expat-2.0.1_5, linux-c6-fontconfig-2.8.0_3, linux-c6-xorg-libs-7.4_10, linux_base-c6-6.10_1, perl5-5.28.2, phrap-1.090518, phred-0.020425.c

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_4, 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_1,1, ca_root_nss-3.44, cairo-1.16.0,2, colord-1.3.5, cups-2.2.11, dbus-1.12.12, dbus-glib-0.110, dconf-0.28.0, dejavu-2.37_1, enchant2-2.2.3_3, encodings-1.0.4_4,1, 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, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gconf2-3.2.6_5, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, geoclue-2.4.7, gettext-runtime-0.19.8.1_2, giflib-5.1.8, glib-2.56.3_5,1, glib-networking-2.56.1_1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphene-1.8.2_1, graphite2-1.3.13, gsettings-desktop-schemas-3.28.1, gstreamer1-1.14.4, gstreamer1-plugins-1.14.4_1, gstreamer1-plugins-bad-1.14.4, gstreamer1-plugins-gl-1.14.4_2, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, gtk3-3.24.7, harfbuzz-2.4.0_1, harfbuzz-icu-2.4.0_1, hicolor-icon-theme-0.17, hunspell-1.7.0_1, 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-1.0.9_3,1, libIDL-0.8.14_4, libSM-1.2.3,1, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libcroco-0.6.12, libdaemon-0.14_1, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libepoxy-1.5.2, libffi-3.2.1_3, libfontenc-1.1.4, libgcrypt-1.8.4_1, libgpg-error-1.36, libgsf-1.14.44, libiconv-1.14_11, libidn2-2.1.1, libmspack-0.9.1, libnotify-0.7.7_1, libpaper-1.1.24.4, libpciaccess-0.13.5, libproxy-0.4.15, libpthread-stubs-0.4, librsvg2-2.40.20, libsecret-0.18.6_1, libsoup-2.62.3, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxkbcommon-0.8.0_1, libxml2-2.9.8, libxshmfence-1.2_4, libxslt-1.1.32, mesa-libs-18.3.2, mkfontscale-1.2.1, nettle-3.4.1_1, nspr-4.21, openjpeg-2.3.1, orc-0.4.28, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, perl5-5.28.2, pixman-0.34.0_1, png-1.6.37, polkit-0.114_2, py27-wxPython-common-3.0.2.0_7, py27-wxPython30-3.0.2.0_7, py35-setuptools-41.0.0, py36-cairo-1.14.1, py36-gobject3-3.28.3, pygobject3-common-3.28.3, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, shared-mime-info-1.10_1, spidermonkey52-52.9.0_3, sqlite3-3.28.0, tiff-4.0.10, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, wayland-protocols-1.17, webkit2-gtk3-2.24.0_1, webp-1.0.2, woff2-1.0.2_3, wx30-gtk3-3.0.4_7, xkeyboard-config-2.24_1, xorg-fonts-truetype-7.7_1, xorgproto-2018.4
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-5.0.7, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, gettext-runtime-0.19.8.1_2, giflib-5.1.8, indexinfo-0.3.1, java-zoneinfo-2019.a, javavmwrapper-2.6, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, maven-3.6.0, maven-wrapper-1_2, mkfontscale-1.2.1, openjdk8-8.212.4.1, xorgproto-2018.4
Also listed in: Java

dDocent-2.7.8
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-5.0.7, bedtools-2.27.1_2, binutils-2.32,1, bwa-0.7.17, ca_root_nss-3.44, cairo-1.16.0,2, cd-hit-4.8.1, coreutils-8.31, cups-2.2.11, curl-7.64.1_1, dbus-1.12.12, dbus-glib-0.110, dconf-0.28.0, dejavu-2.37_1, encodings-1.0.4_4,1, expat-2.2.6_1, fastahack-g20160702, fastp-0.20.0, filevercmp-g20151117, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, font-util-1.3.1, fontconfig-2.12.6,1, freebayes-1.2.0_1, freetype2-2.9.1, fribidi-0.19.7, fsom-g20151117_1, gawk-5.0.0, gcc8-8.3.0_2, gconf2-3.2.6_5, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, giflib-5.1.8, glib-2.56.3_5,1, gmp-6.1.2_1, gnome_subr-1.0, gnuplot-5.2.6_1, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, gstreamer-0.10.36_6, gstreamer-plugins-0.10.36_12,3, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.4.0_1, hicolor-icon-theme-0.17, htslib-1.9, icu-64.2,1, indexinfo-0.3.1, intervaltree-g20151213_1, java-zoneinfo-2019.a, javavmwrapper-2.6, jbigkit-2.1_1, jpeg-turbo-2.0.2, jsoncpp-1.8.1_6, libGLU-9.0.0_3, libICE-1.0.9_3,1, libIDL-0.8.14_4, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libXv-1.0.11_2,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libedit-3.1.20181209_2,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libgd-2.2.5_1,1, libiconv-1.14_11, libidn2-2.1.1, libinotify-20180201_1, libmspack-0.9.1, libnghttp2-1.38.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libsigsegv-2.12, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, lua53-5.3.5_3, mawk-1.3.4.20161120, mesa-libs-18.3.2, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, multichoose-1.0.3.2, nettle-3.4.1_1, nspr-4.21, openjdk8-8.212.4.1, orc-0.4.28, p11-kit-0.23.15, pango-1.42.4_2, pangox-compat-0.0.2_2, parallel-20180922, pciids-20190418, pcre-8.43_1, pear-merger-0.9.6, perl5-5.28.2, pixman-0.34.0_1, png-1.6.37, polkit-0.114_2, python36-3.6.8_2, 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_3, stacks-2.4, tabixpp-1.0.0.10, tex-kpathsea-6.2.1_2, tiff-4.0.10, tpm-emulator-0.7.4_2, trimadap-0.1.3, trimmomatic-0.35, trousers-0.3.14_2, unzip-6.0_7, vcflib-1.0.0.r1.130, vcftools-0.1.16, wayland-1.16.0_1, webp-1.0.2, wx28-gtk2-2.8.12_7, wx28-gtk2-common-2.8.12_7, xorg-fonts-truetype-7.7_1, xorgproto-2018.4
Also listed in: Java, Perl5, Python

diamond-0.9.24
BLAST-compatible local sequence aligner
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: ca_root_nss-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, gettext-runtime-0.19.8.1_2, indexinfo-0.3.1, jsoncpp-1.8.1_6, libarchive-3.3.3,1, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.8_2, readline-8.0.0, rhash-1.3.5

dsr-pdb-1.0.3_2
Simple C++ PDB reader (reads the protein description format)
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: boost-libs-1.70.0_2, gettext-runtime-0.19.8.1_2, 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, freetype2-2.9.1, gettext-runtime-0.19.8.1_2, giflib-5.1.8, gmake-4.2.1_3, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXaw-1.0.13_2,2, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXft-2.3.2_3, libXmu-1.1.2_5,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libgd-2.2.5_1,1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, open-motif-2.3.8, png-1.6.37, primer3-2.3.6, tiff-4.0.10, webp-1.0.2, xbitmaps-1.1.2, xorgproto-2018.4

exonerate-2.4.0
Generic tool for sequence alignment
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: gettext-runtime-0.19.8.1_2, glib-2.56.3_5,1, indexinfo-0.3.1, libffi-3.2.1_3, libiconv-1.14_11, libxml2-2.9.8, pcre-8.43_1, pkgconf-1.6.1,1, python36-3.6.8_2, 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
Ultra-fast all-in-one FASTQ preprocessor
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_2, 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, freetype2-2.9.1, giflib-5.1.8, java-zoneinfo-2019.a, javavmwrapper-2.6, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, mkfontscale-1.2.1, openjdk8-8.212.4.1, perl5-5.28.2, xorgproto-2018.4
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_2, autoconf-wrapper-20131203, automake-1.16.1_1, indexinfo-0.3.1, libgtextutils-0.7, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.28.2, pkgconf-1.6.1,1

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-1.10.5, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, java-zoneinfo-2019.a, javavmwrapper-2.6, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, mkfontscale-1.2.1, openjdk8-8.212.4.1, xorgproto-2018.4
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_1
Bayesian haplotype-based polymorphism discovery and genotyping
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_2, 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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, xorgproto-2018.4

gatk-4.0.11.0
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, freetype2-2.9.1, gettext-runtime-0.19.8.1_2, giflib-5.1.8, gradle4-4.6, indexinfo-0.3.1, java-zoneinfo-2019.a, javavmwrapper-2.6, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, mkfontscale-1.2.1, openjdk8-8.212.4.1, xorgproto-2018.4
Also listed in: Java

gemma-0.98.1
Genome-wide Efficient Mixed Model Association
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32,1, cblas-1.0_11, eigen-3.3.7, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, 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_8,1

gff2ps-0.98l
Converts gff-formated genomic data-sets to PostScript
Long description | Changes | Main Web Site
Maintained by: egypcio@FreeBSD.org
Requires: bash-5.0.7, gawk-5.0.0, gettext-runtime-0.19.8.1_2, 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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, perl5-5.28.2

gperiodic-2.0.10_8
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-3.44, cairo-1.16.0,2, cups-2.2.11, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.4_4,1, 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, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, gettext-tools-0.19.8.1_1, glib-2.56.3_5,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.4.0_1, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libiconv-1.14_11, libidn2-2.1.1, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, mesa-libs-18.3.2, mkfontscale-1.2.1, nettle-3.4.1_1, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, pixman-0.34.0_1, pkgconf-1.6.1,1, png-1.6.37, python36-3.6.8_2, readline-8.0.0, shared-mime-info-1.10_1, tiff-4.0.10, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xorg-fonts-truetype-7.7_1, xorgproto-2018.4

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-0.19.8.1_2, 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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1

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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, perl5-5.28.2, python36-3.6.8_2, readline-8.0.0
Also listed in: Perl5, Python

hmmer-3.2.1
Profile hidden Markov models for biological sequence analysis
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: gettext-runtime-0.19.8.1_2, 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_2, autoconf-wrapper-20131203, automake-1.16.1_1, ca_root_nss-3.44, curl-7.64.1_1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libnghttp2-1.38.0, m4-1.4.18_1,1, perl5-5.28.2
Also listed in: Devel

hyphy-2.3.14.16_1
Hypothesis testing using Phylogenies
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: ca_root_nss-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, gettext-runtime-0.19.8.1_2, indexinfo-0.3.1, jsoncpp-1.8.1_6, libarchive-3.3.3,1, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.8_2, readline-8.0.0, rhash-1.3.5

igv-2.5.2
Visualization tool for genomic datasets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: alsa-lib-1.1.2_2, atk-2.28.1, avahi-app-0.7_2, ca_root_nss-3.44, cairo-1.16.0,2, cups-2.2.11, dav1d-0.3.1, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.4_4,1, expat-2.2.6_1, ffmpeg-4.1.3_6,1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, giflib-5.1.8, glib-2.56.3_5,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, gradle4-4.6, graphite2-1.3.13, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.4.0_1, hicolor-icon-theme-0.17, icu-64.2,1, indexinfo-0.3.1, java-zoneinfo-2019.a, javavmwrapper-2.6, jbigkit-2.1_1, jpeg-turbo-2.0.2, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libgcrypt-1.8.4_1, libgpg-error-1.36, libiconv-1.14_11, libidn2-2.1.1, libinotify-20180201_1, libogg-1.3.3,4, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libtheora-1.1.1_7, libunistring-0.9.10_1, libunwind-20170615, libv4l-1.6.3_4, libva-2.4.1_1, libvdpau-1.1.1_2, libvorbis-1.3.6,3, libvpx-1.8.0, libx264-0.157.2945, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, libxslt-1.1.32, mesa-libs-18.3.2, mkfontscale-1.2.1, nettle-3.4.1_1, opencv-core-3.4.1_17, openjdk8-8.212.4.1, openjfx8-devel-8.u172.b11_7,1, opus-1.3.1, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, pixman-0.34.0_1, png-1.6.37, python36-3.6.8_2, readline-8.0.0, shared-mime-info-1.10_1, sndio-1.5.0, sqlite3-3.28.0, tiff-4.0.10, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, x265-3.0_1, xorg-fonts-truetype-7.7_1, xorgproto-2018.4, 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-0.19.8.1_2, 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_2, autoconf-wrapper-20131203, automake-1.16.1_1, ca_root_nss-3.44, curl-7.64.1_1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libnghttp2-1.38.0, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.28.2

iqtree-1.6.10
Efficient phylogenomic software by maximum likelihood
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.32,1, ca_root_nss-3.44, cmake-3.14.4, curl-7.64.1_1, eigen-3.3.7, expat-2.2.6_1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, jsoncpp-1.8.1_6, libarchive-3.3.3,1, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.0.2, ninja-1.9.0,2, python36-3.6.8_2, 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-1.10.5, dejavu-2.37_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, java-zoneinfo-2019.a, javavmwrapper-2.6, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, mkfontscale-1.2.1, openjdk8-8.212.4.1, xorgproto-2018.4
Also listed in: Java

kallisto-0.45.1
Quantify abundances of transcripts from RNA-Seq data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, hdf-szip-2.1.1, hdf5-1.10.5_1, htslib-1.9, jsoncpp-1.8.1_6, libarchive-3.3.3,1, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, 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: perl5-5.28.2

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

libgtextutils-0.7
Gordon's text utilities
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_2, autoconf-wrapper-20131203, automake-1.16.1_1, indexinfo-0.3.1, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.28.2, pkgconf-1.6.1,1

libsbml-5.17.0
API Library for Working with SBML File
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, gettext-runtime-0.19.8.1_2, indexinfo-0.3.1, jsoncpp-1.8.1_6, libarchive-3.3.3,1, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, libxml2-2.9.8, lzo2-2.10_1, ninja-1.9.0,2, python36-3.6.8_2, 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-c6-6.10_1

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-0.19.8.1_2, 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_2, autoconf-wrapper-20131203, automake-1.16.1_1, bash-5.0.7, bison-3.3.2,1, ca_root_nss-3.44, curl-7.64.1_1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, hdf-szip-2.1.1, hdf5-1.10.5_1, indexinfo-0.3.1, libnghttp2-1.38.0, libtool-2.4.6_1, m4-1.4.18_1,1, netcdf-4.7.0, perl5-5.28.2, pkgconf-1.6.1,1
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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1

mmtf-cpp-1.0.0_1
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-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, gettext-runtime-0.19.8.1_2, indexinfo-0.3.1, jsoncpp-1.8.1_6, libarchive-3.3.3,1, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, lzo2-2.10_1, msgpack-3.1.1_1, ninja-1.9.0,2, python36-3.6.8_2, readline-8.0.0, rhash-1.3.5
Also listed in: Science

molden-5.8.2_2
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, expat-2.2.6_1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, libGLU-9.0.0_3, libX11-1.6.7,1, libXau-1.0.9, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXxf86vm-1.1.4_3, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, mesa-libs-18.3.2, mpc-1.1.0_2, mpfr-4.0.2, pciids-20190418, wayland-1.16.0_1, xorgproto-2018.4

mopac-7.1.15_7
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.32,1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2

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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, readline-8.0.0

mummer-4.0.0.b2.2_1
Modular system for rapid whole genome alignment
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: autoconf-2.69_2, autoconf-wrapper-20131203, automake-1.16.1_1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libedit-3.1.20181209_2,1, libffi-3.2.1_3, libtool-2.4.6_1, libunwind-20170615, libyaml-0.2.2, m4-1.4.18_1,1, perl5-5.28.2, ruby-2.5.5_2,1, 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-2.8.1_2
NCBI implementation of Basic Local Alignment Search Tool
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32,1, ca_root_nss-3.44, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, gmp-6.1.2_1, gnutls-3.6.7, indexinfo-0.3.1, libffi-3.2.1_3, libgcrypt-1.8.4_1, libgpg-error-1.36, libidn2-2.1.1, libtasn1-4.13_1, libunistring-0.9.10_1, lmdb-0.9.23,1, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.4.1_1, p11-kit-0.23.15, p5-Exporter-Tiny-1.002001, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, pcre-8.43_1, perl5-5.28.2, python36-3.6.8_2, readline-8.0.0, sqlite3-3.28.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2
Also listed in: Perl5, Python

ncbi-cxx-toolkit-21.0.0_1
NCBI C++ Toolkit
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: bash-5.0.7, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXpm-3.5.12_2, libXt-1.1.5_2,1, libedit-3.1.20181209_2,1, libevent-2.1.8_3, libffi-3.2.1_3, liblz4-1.9.1,1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, mysql56-client-5.6.44, pcre-8.43_1, perl5-5.28.2, python36-3.6.8_2, readline-8.0.0, xorgproto-2018.4
Also listed in: Science, Devel

ncbi-toolkit-2017.01.06_2
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-3.44, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, gnutls-3.6.7, indexinfo-0.3.1, jpeg-turbo-2.0.2, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXaw-1.0.13_2,2, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXft-2.3.2_3, libXmu-1.1.2_5,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libffi-3.2.1_3, libidn2-2.1.1, libpthread-stubs-0.4, libtasn1-4.13_1, libunistring-0.9.10_1, libxcb-1.13.1, libxml2-2.9.8, nettle-3.4.1_1, open-motif-2.3.8, p11-kit-0.23.15, png-1.6.37, tpm-emulator-0.7.4_2, trousers-0.3.14_2, xbitmaps-1.1.2, xorgproto-2018.4

nest-2.16.0
Simulator for spiking neural network models
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ca_root_nss-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, gettext-runtime-0.19.8.1_2, gsl-2.5_1, indexinfo-0.3.1, jsoncpp-1.8.1_6, libarchive-3.3.3,1, libffi-3.2.1_3, libltdl-2.4.6, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, lzo2-2.10_1, ninja-1.9.0,2, openmp-8.0.0_1, pkgconf-1.6.1,1, py35-cython-0.29_1, py35-setuptools-41.0.0, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, rhash-1.3.5
Also listed in: Science

ngs-sdk-2.9.6
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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, perl5-5.28.2

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-0.17027, 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, perl5-5.28.2
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, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libxml2-2.9.8, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007005, p5-Class-Data-Inheritable-0.08_1, p5-DBI-1.642, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17027, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, 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-6.04, 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-6.18, 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-1.00, 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, perl5-5.28.2, png-1.6.37, tiff-4.0.10, webp-1.0.2
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, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libxml2-2.9.8, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007005, p5-Class-Data-Inheritable-0.08_1, p5-DBI-1.642, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17027, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, 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-6.04, 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-6.18, 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-1.00, 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, perl5-5.28.2, png-1.6.37, tiff-4.0.10, webp-1.0.2
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, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libxml2-2.9.8, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007005, p5-Class-Data-Inheritable-0.08_1, p5-DBI-1.642, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17027, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, 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-6.04, 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-6.18, 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-1.00, 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, perl5-5.28.2, png-1.6.37, tiff-4.0.10, webp-1.0.2
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, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libxml2-2.9.8, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007005, p5-Class-Data-Inheritable-0.08_1, p5-DBI-1.642, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17027, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, 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-6.04, 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-6.18, 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-1.00, 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, perl5-5.28.2, png-1.6.37, tiff-4.0.10, webp-1.0.2
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-3.44, curl-7.64.1_1, libnghttp2-1.38.0, 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-6.04, 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-6.18, 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, perl5-5.28.2
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, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libxml2-2.9.8, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007005, p5-Class-Data-Inheritable-0.08_1, p5-DBI-1.642, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17027, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, 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-6.04, 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-6.18, 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-1.00, 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, perl5-5.28.2, png-1.6.37, tiff-4.0.10, webp-1.0.2
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, perl5-5.28.2
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-6.04, 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-6.18, 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, perl5-5.28.2
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-3.44, curl-7.64.1_1, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, io_lib-1.14.10, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libnghttp2-1.38.0, libxml2-2.9.8, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Bio-Coordinate-1.007001, p5-Bio-SCF-1.03_2, p5-BioPerl-1.007005, p5-CGI-4.43, p5-Class-Data-Inheritable-0.08_1, p5-DBI-1.642, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17027, 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-6.04, 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-6.18, 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-1.00, 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, perl5-5.28.2, png-1.6.37, tiff-4.0.10, webp-1.0.2
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-1.34, p5-Class-Load-0.25, p5-Class-Load-XS-0.10, p5-Class-Method-Modifiers-2.12, p5-Class-Singleton-1.5_1, p5-Data-OptList-0.110, p5-Date-Manip-6.76, p5-DateTime-1.51, p5-DateTime-Format-DateManip-0.04_1, p5-DateTime-Locale-1.24, p5-DateTime-TimeZone-2.35,1, p5-Devel-GlobalDestruction-0.14, p5-Devel-OverloadInfo-0.005, p5-Devel-StackTrace-2.03, 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-1.20,1, 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-2.000006, p5-Scalar-List-Utils-1.50,1, p5-Specio-0.43, 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-0.28, p5-namespace-clean-0.27, perl5-5.28.2
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, perl5-5.28.2
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, freetype2-2.9.1, giflib-5.1.8, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libxml2-2.9.8, p5-Algorithm-C3-0.10_1, p5-Algorithm-Combinatorics-0.27_1, p5-Algorithm-Diff-1.1903, p5-Archive-Zip-1.64, p5-Authen-NTLM-1.09_1, p5-B-Hooks-EndOfScope-0.24, p5-B-Hooks-OP-Check-0.22, p5-BioPerl-1.007005, p5-Cache-LRU-0.04_1, p5-Class-C3-0.34, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.34, p5-Class-Load-0.25, p5-Class-Load-XS-0.10, p5-Class-Method-Modifiers-2.12, p5-Class-Singleton-1.5_1, p5-DBD-SQLite-1.62, 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-2.35,1, p5-Devel-GlobalDestruction-0.14, p5-Devel-OverloadInfo-0.005, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Dist-CheckConflicts-0.11_1, p5-Encode-Locale-1.05, p5-Error-0.17027, 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-6.04, 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-6.18, p5-Net-SSLeay-1.85, p5-PDF-API2-2.033, 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-2.000006, p5-SVG-2.84, p5-SWF-Builder-0.16_2, p5-SWF-File-0.42_2,1, p5-Scalar-List-Utils-1.50,1, p5-Set-Scalar-1.29, p5-Socket6-0.29, p5-Specio-0.43, 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-0.014, 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-1.00, 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-0.006, p5-indirect-0.33, p5-libwww-6.39, p5-libxml-0.08_1, p5-multidimensional-0.014, p5-namespace-autoclean-0.28, p5-namespace-clean-0.27, p5-strictures-2.000006,1, perl5-5.28.2, png-1.6.37, tiff-4.0.10, webp-1.0.2
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-3.44, curl-7.64.1_1, io_lib-1.14.10, libnghttp2-1.38.0, perl5-5.28.2
Also listed in: Perl5

p5-BioPerl-1.007005
Collection of Perl modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: sunpoet@FreeBSD.org
Requires: expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libxml2-2.9.8, p5-Algorithm-Diff-1.1903, p5-Authen-NTLM-1.09_1, p5-Class-Data-Inheritable-0.08_1, p5-DBI-1.642, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17027, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.002001, p5-File-Listing-6.04_1, 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-6.04, 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-6.18, 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-1.00, 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, perl5-5.28.2, png-1.6.37, tiff-4.0.10, webp-1.0.2
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, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.8, jbigkit-2.1_1, jpeg-turbo-2.0.2, libgd-2.2.5_1,1, libiconv-1.14_11, libxml2-2.9.8, 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-1.007005, p5-Class-Data-Inheritable-0.08_1, p5-Config-Any-0.32, p5-Config-General-2.63, p5-Config-Tiny-2.23, p5-Cpanel-JSON-XS-4.11, p5-DBI-1.642, p5-Data-Stag-0.14_2, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Encode-Locale-1.05, p5-Error-0.17027, 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-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-6.04, 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-6.18, 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-1.00, 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-0.77, p5-libwww-6.39, p5-libxml-0.08_1, perl5-5.28.2, png-1.6.37, tiff-4.0.10, webp-1.0.2
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, freetype2-2.9.1, gettext-runtime-0.19.8.1_2, giflib-5.1.8, indexinfo-0.3.1, java-zoneinfo-2019.a, javavmwrapper-2.6, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, 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, libxml2-2.9.8, mkfontscale-1.2.1, openjdk8-8.212.4.1, perl5-5.28.2, py27-bz2file-0.98, py35-setuptools-41.0.0, py36-cutadapt-2.3, py36-dnaio-0.3, py36-xopen-0.5.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, xorgproto-2018.4
Also listed in: Perl5, Python

p5-transdecoder-5.4.0_1
Identify candidate coding regions within transcript sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32,1, cd-hit-4.8.1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2, p5-URI-1.76, perl5-5.28.2
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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1

pbbam-0.18.0_1
PacBio BAM C++ library, with SWIG bindings
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: boost-libs-1.70.0_2, ca_root_nss-3.44, curl-7.64.1_1, gettext-runtime-0.19.8.1_2, htslib-1.9, icu-64.2,1, indexinfo-0.3.1, libffi-3.2.1_3, libnghttp2-1.38.0, meson-0.50.0, ninja-1.9.0,2, pkgconf-1.6.1,1, py35-setuptools-41.0.0, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0

pbcopper-0.4.1_1
Core C++ library for Pacific Biosciences tools
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: boost-libs-1.70.0_2, gettext-runtime-0.19.8.1_2, icu-64.2,1, indexinfo-0.3.1, libffi-3.2.1_3, meson-0.50.0, ninja-1.9.0,2, py35-setuptools-41.0.0, python35-3.5.7_2, python36-3.6.8_2, 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-5.0.7, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXaw-1.0.13_2,2, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXmu-1.1.2_5,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXt-1.1.5_2,1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, xorgproto-2018.4

phyml-3.3.20180621_1
Simple, fast, and accurate algorithm to estimate large phylogenies
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69_2, autoconf-wrapper-20131203, automake-1.16.1_1, indexinfo-0.3.1, libtool-2.4.6_1, m4-1.4.18_1,1, perl5-5.28.2, pkgconf-1.6.1,1

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-0.19.8.1_2, 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-0.19.8.1_2, 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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1

prodigy-lig-1.0.0.3
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, blas-3.5.0_5, cblas-1.0_11, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, giflib-5.1.8, 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_7, lcms2-2.9, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, 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, libxml2-2.9.8, metis-5.1.0_7, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, openjpeg-2.3.1, png-1.6.37, py27-biopython-1.73, py27-numpy-1.16.1_2,1, py27-pillow-5.3.0, py27-reportlab-3.5.21, py35-setuptools-41.0.0, py36-tkinter-3.6.8_6, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, suitesparse-5.2.0_3, tcl86-8.6.9_1, tiff-4.0.10, tk86-8.6.9_1, webp-1.0.2, xorgproto-2018.4
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-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXmu-1.1.2_5,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXxf86vm-1.1.4_3, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, mesa-libs-18.3.2, pciids-20190418, png-1.6.37, tiff-4.0.10, wayland-1.16.0_1, xorgproto-2018.4

psi88-1.0_15
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.32,1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, 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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py27-cffi-1.12.3, py27-idna-2.8, py27-ipaddress-1.0.22, py27-openssl-18.0.0, py27-pycparser-2.18, py27-pysocks-1.6.8, py27-requests-2.21.0, py27-six-1.12.0, py27-urllib3-1.22,1, py35-setuptools-41.0.0, py36-asn1crypto-0.22.0, py36-certifi-2019.3.9, py36-chardet-3.0.4_1, py36-cryptography-2.6.1, py36-slumber-0.7.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0
Also listed in: Python

py27-biom-format-2.1.7_2
Biological Observation Matrix (BIOM) Format Project
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.32,1, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, hdf-szip-2.1.1, hdf5-1.10.5_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, perl5-5.28.2, postgresql95-client-9.5.17_1, py27-bottleneck-1.2.1_4, py27-dateutil-2.7.3, py27-future-0.17.1_1, py27-numexpr-2.6.9, py27-numpy-1.16.1_2,1, py27-pyqi-0.3.2_1, py27-pytz-2019.1,1, py27-six-1.12.0, py35-setuptools-41.0.0, py36-click-7.0, py36-h5py-2.9.0_1, py36-pandas-0.24.2, py36-scipy-1.2.0_1, py36-sqlite3-3.6.8_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, sqlite3-3.28.0, suitesparse-5.2.0_3
Also listed in: Python

py27-biopython-1.73
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, blas-3.5.0_5, cblas-1.0_11, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, giflib-5.1.8, gmp-6.1.2_1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_7, lcms2-2.9, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, 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, libxml2-2.9.8, metis-5.1.0_7, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, openjpeg-2.3.1, png-1.6.37, py27-numpy-1.16.1_2,1, py27-pillow-5.3.0, py27-reportlab-3.5.21, py35-setuptools-41.0.0, py36-tkinter-3.6.8_6, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, suitesparse-5.2.0_3, tcl86-8.6.9_1, tiff-4.0.10, tk86-8.6.9_1, webp-1.0.2, xorgproto-2018.4
Also listed in: Python

py27-bx-python-0.8.2_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, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, lzo2-2.10_1, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-numpy-1.16.1_2,1, py27-python-lzo-1.12, py35-cython-0.29_1, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, readline-8.0.0, suitesparse-5.2.0_3
Also listed in: Python

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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py27-argcomplete-1.10.0, py27-argh-0.26.1, py27-six-1.12.0, py35-setuptools-41.0.0, py36-pyfaidx-0.5.5.2_1, py36-simplejson-3.16.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0
Also listed in: Python

py27-gtfparse-1.2.0_1
Parsing tools for GTF (gene transfer format) files
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32,1, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-bottleneck-1.2.1_4, py27-dateutil-2.7.3, py27-numexpr-2.6.9, py27-numpy-1.16.1_2,1, py27-pytz-2019.1,1, py27-six-1.12.0, py35-setuptools-41.0.0, py36-pandas-0.24.2, py36-sqlite3-3.6.8_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, sqlite3-3.28.0, suitesparse-5.2.0_3
Also listed in: Python

py27-macs2-2.1.0.p20170505_2
Analysis of chromatin immunoprecipitation (ChIP) sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32,1, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-numpy-1.16.1_2,1, py35-cython-0.29_1, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, readline-8.0.0, suitesparse-5.2.0_3
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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py27-six-1.12.0, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, readline-8.0.0
Also listed in: Python

py27-pyfasta-0.5.2_3
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, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-numpy-1.16.1_2,1, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, readline-8.0.0, suitesparse-5.2.0_3
Also listed in: Python

py27-pymol-2.3.0
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, blas-3.5.0_5, blt-2.5.3_3, ca_root_nss-3.44, cairo-1.16.0,2, cblas-1.0_11, cups-2.2.11, 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, freetype2-2.9.1, gcc8-8.3.0_2, gdbm-1.18.1_1, gettext-runtime-0.19.8.1_2, giflib-5.1.8, glew-2.1.0, glib-2.56.3_5,1, glm-0.9.8.5_3,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, harfbuzz-2.4.0_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_7, lcms-1.19_6,1, libGLU-9.0.0_3, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXfontcache-1.0.5_5, libXft-2.3.2_3, libXi-1.7.9_2,1, libXmu-1.1.2_5,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libiconv-1.14_11, libidn2-2.1.1, libmng-1.0.10_3, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxkbcommon-0.8.0_1, libxml2-2.9.8, libxshmfence-1.2_4, mesa-libs-18.3.2, metis-5.1.0_7, mmtf-cpp-1.0.0_1, mpc-1.1.0_2, mpfr-4.0.2, msgpack-3.1.1_1, nettle-3.4.1_1, openblas-0.2.20_8,1, p11-kit-0.23.15, pciids-20190418, pcre-8.43_1, pcre2-10.32_1, pixman-0.34.0_1, png-1.6.37, py27-enum34-1.1.6, py27-msgpack-0.6.1, py27-numpy-1.16.1_2,1, py27-qt5-gui-5.12.2, py27-qt5-opengl-5.12.2, py27-qt5-widgets-5.12.2, py27-sip-4.19.17,1, py35-setuptools-41.0.0, py36-Pmw-2.0.1, py36-qt5-core-5.12.2, py36-tkinter-3.6.8_6, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, qscintilla2-qt5-2.11.1, qt5-core-5.12.2_1, qt5-dbus-5.12.2, qt5-gui-5.12.2, qt5-imageformats-5.12.2, qt5-network-5.12.2_1, qt5-opengl-5.12.2, qt5-printsupport-5.12.2, qt5-widgets-5.12.2, qtchooser-66, readline-8.0.0, suitesparse-5.2.0_3, tcl86-8.6.9_1, tiff-4.0.10, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.2, 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-2.24_1, xorgproto-2018.4, xprop-1.2.4, xset-1.2.4_2
Also listed in: Science, Python

py27-pysam-0.15.2
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, py35-cython-0.29_1, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, 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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.0.0, 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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.0.0, 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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py27-cffi-1.12.3, py27-idna-2.8, py27-ipaddress-1.0.22, py27-openssl-18.0.0, py27-pycparser-2.18, py27-pysocks-1.6.8, py27-requests-2.21.0, py27-six-1.12.0, py27-urllib3-1.22,1, py35-setuptools-41.0.0, py36-asn1crypto-0.22.0, py36-certifi-2019.3.9, py36-chardet-3.0.4_1, py36-cryptography-2.6.1, py36-slumber-0.7.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0
Also listed in: Python

py36-biom-format-2.1.7_2
Biological Observation Matrix (BIOM) Format Project
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.32,1, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, hdf-szip-2.1.1, hdf5-1.10.5_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-bottleneck-1.2.1_4, py27-dateutil-2.7.3, py27-future-0.17.1_1, py27-numexpr-2.6.9, py27-numpy-1.16.1_2,1, py27-pytz-2019.1,1, py27-six-1.12.0, py35-setuptools-41.0.0, py36-click-7.0, py36-h5py-2.9.0_1, py36-pandas-0.24.2, py36-scipy-1.2.0_1, py36-sqlite3-3.6.8_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, sqlite3-3.28.0, suitesparse-5.2.0_3
Also listed in: Python

py36-biopython-1.73
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, blas-3.5.0_5, cblas-1.0_11, expat-2.2.6_1, fontconfig-2.12.6,1, freetype2-2.9.1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, giflib-5.1.8, gmp-6.1.2_1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, lapack-3.5.0_7, lcms2-2.9, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, 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, libxml2-2.9.8, metis-5.1.0_7, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, openjpeg-2.3.1, png-1.6.37, py27-numpy-1.16.1_2,1, py27-pillow-5.3.0, py27-reportlab-3.5.21, py35-setuptools-41.0.0, py36-tkinter-3.6.8_6, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, suitesparse-5.2.0_3, tcl86-8.6.9_1, tiff-4.0.10, tk86-8.6.9_1, webp-1.0.2, xorgproto-2018.4
Also listed in: Python

py36-bx-python-0.8.2_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, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, lzo2-2.10_1, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-numpy-1.16.1_2,1, py27-python-lzo-1.12, py35-cython-0.29_1, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, suitesparse-5.2.0_3
Also listed in: Python

py36-cutadapt-2.3
Trim adapters from high-throughput sequencing reads
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py27-bz2file-0.98, py27-setuptools_scm-3.1.0, py35-cython-0.29_1, py35-setuptools-41.0.0, py36-dnaio-0.3, py36-xopen-0.5.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0
Also listed in: Python

py36-deap-1.2.2_1
Distributed Evolutionary Algorithms in Python
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32,1, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-numpy-1.16.1_2,1, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, suitesparse-5.2.0_3
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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.0.0, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0
Also listed in: Python

py36-fastTSNE-0.2.13_1
Fast, parallel implementations of t-SNE
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32,1, blas-3.5.0_5, cblas-1.0_11, fftw3-3.3.8_3, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libedit-3.1.20181209_2,1, libffi-3.2.1_3, libxml2-2.9.8, llvm60-6.0.1_6, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, openmp-8.0.0_1, perl5-5.28.2, py27-numpy-1.16.1_2,1, py27-scikit-learn-0.20.3, py35-setuptools-41.0.0, py36-llvmlite-0.25.0_2, py36-numba-0.40.1_4, py36-scipy-1.2.0_1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, suitesparse-5.2.0_3, 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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py27-argcomplete-1.10.0, py27-argh-0.26.1, py27-six-1.12.0, py35-setuptools-41.0.0, py36-pyfaidx-0.5.5.2_1, py36-simplejson-3.16.1, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0
Also listed in: Python

py36-gtfparse-1.2.0_1
Parsing tools for GTF (gene transfer format) files
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32,1, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-bottleneck-1.2.1_4, py27-dateutil-2.7.3, py27-numexpr-2.6.9, py27-numpy-1.16.1_2,1, py27-pytz-2019.1,1, py27-six-1.12.0, py35-setuptools-41.0.0, py36-pandas-0.24.2, py36-sqlite3-3.6.8_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, sqlite3-3.28.0, suitesparse-5.2.0_3
Also listed in: Python

py36-loompy-2.0.17
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, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, hdf-szip-2.1.1, hdf5-1.10.5_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-bottleneck-1.2.1_4, py27-dateutil-2.7.3, py27-numexpr-2.6.9, py27-numpy-1.16.1_2,1, py27-pytz-2019.1,1, py27-six-1.12.0, py35-setuptools-41.0.0, py36-h5py-2.9.0_1, py36-pandas-0.24.2, py36-scipy-1.2.0_1, py36-sqlite3-3.6.8_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, sqlite3-3.28.0, suitesparse-5.2.0_3
Also listed in: Python

py36-orange3-bioinformatics-3.2.2_2
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_4, atk-2.28.1, avahi-app-0.7_2, binutils-2.32,1, blas-3.5.0_5, ca_root_nss-3.44, cairo-1.16.0,2, cblas-1.0_11, cups-2.2.11, dav1d-0.3.1, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.4_4,1, etc_os-release-0.1_2, expat-2.2.6_1, ffmpeg-4.1.3_6,1, fftw3-3.3.8_3, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, font-util-1.3.1, fontconfig-2.12.6,1, freeglut-3.0.0_2, freetype2-2.9.1, fribidi-0.19.7, gcc8-8.3.0_2, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, giflib-5.1.8, glib-2.56.3_5,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, graphviz-2.40.1_9, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.4.0_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_6, lapack-3.5.0_7, lcms-1.19_6,1, lcms2-2.9, libGLU-9.0.0_3, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_2,2, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXfontcache-1.0.5_5, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXmu-1.1.2_5,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libedit-3.1.20181209_2,1, libepoll-shim-0.0.20190311, libevent-2.1.8_3, libffi-3.2.1_3, libfontenc-1.1.4, libgcrypt-1.8.4_1, libgd-2.2.5_1,1, libglade2-2.6.4_9, libgpg-error-1.36, libiconv-1.14_11, libidn2-2.1.1, libltdl-2.4.6, libmng-1.0.10_3, libogg-1.3.3,4, libpaper-1.1.24.4, libpci-3.6.2, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libtheora-1.1.1_7, libunistring-0.9.10_1, libunwind-20170615, libv4l-1.6.3_4, libva-2.4.1_1, libvdpau-1.1.1_2, libvorbis-1.3.6,3, libvpx-1.8.0, libx264-0.157.2945, libxcb-1.13.1, libxkbcommon-0.8.0_1, libxml2-2.9.8, libxshmfence-1.2_4, libxslt-1.1.32, llvm60-6.0.1_6, mesa-libs-18.3.2, metis-5.1.0_7, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.4.1_1, nspr-4.21, nss-3.44, openblas-0.2.20_8,1, opencv-core-3.4.1_17, openjpeg-2.3.1, openmp-8.0.0_1, opus-1.3.1, orange3-3.19.0_1, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, pcre2-10.32_1, perl5-5.28.2, pixman-0.34.0_1, png-1.6.37, py27-Genesis-PyAPI-1.2.1, py27-SecretStorage-2.3.1, py27-backports-1, py27-backports.functools_lru_cache-1.5, py27-bottleneck-1.2.1_4, py27-cffi-1.12.3, py27-dateutil-2.7.3, py27-dbus-1.2.8, py27-decorator-4.3.0, py27-docutils-0.14_4, py27-enum34-1.1.6, py27-gobject-2.28.6_8, py27-gtk2-2.24.0_5, py27-idna-2.8, py27-ipaddress-1.0.22, py27-joblib-0.13.0, py27-keyring-12.0.1_1, py27-keyrings.alt-3.1.1, py27-kiwisolver-1.1.0, py27-matplotlib-2.2.4, py27-numpy-1.16.1_2,1, py27-openssl-18.0.0, py27-pillow-5.3.0, py27-pycparser-2.18, py27-pyqtgraph-0.10.0_1, py27-pysocks-1.6.8, py27-python-louvain-0.13_1, py27-pytz-2019.1,1, py27-qt5-gui-5.12.2, py27-qt5-printsupport-5.12.2, py27-qt5-widgets-5.12.2, py27-requests-2.21.0, py27-requests-cache-0.4.13, py27-scikit-learn-0.20.3, py27-scikit-sparse-0.4.4_2, py27-serverfiles-0.3.0, py27-sip-4.19.17,1, py27-six-1.12.0, py27-urllib3-1.22,1, py35-setuptools-41.0.0, py36-AnyQt-0.0.10, py36-PyOpenGL-3.1.0_3, py36-asn1crypto-0.22.0, py36-cairo-1.14.1, py36-certifi-2019.3.9, py36-chardet-3.0.4_1, py36-cryptography-2.6.1, py36-cycler-0.10.0, py36-entrypoints-0.3, py36-fastTSNE-0.2.13_1, py36-llvmlite-0.25.0_2, py36-networkx-2.1_1, py36-numba-0.40.1_4, py36-pygraphviz-1.3.1, py36-pyparsing-2.4.0, py36-qt5-core-5.12.2, py36-qt5-network-5.12.2, py36-qt5-qml-5.12.2, py36-qt5-webchannel-5.12.2, py36-qt5-webengine-5.12.1, py36-scipy-1.2.0_1, py36-slumber-0.7.1, py36-tkinter-3.6.8_6, py36-tornado-5.1.1, py36-xlrd-1.2.0_1, py36-yaml-5.1, pydbus-common-1.2.8, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, qscintilla2-qt5-2.11.1, qt5-assistant-5.12.2, qt5-concurrent-5.12.2, qt5-core-5.12.2_1, qt5-dbus-5.12.2, qt5-declarative-5.12.2, qt5-designer-5.12.2, qt5-gui-5.12.2, qt5-help-5.12.2, qt5-imageformats-5.12.2, qt5-location-5.12.2, qt5-network-5.12.2_1, qt5-printsupport-5.12.2, qt5-serialport-5.12.2, qt5-sql-5.12.2, qt5-sqldrivers-sqlite3-5.12.2, qt5-testlib-5.12.2, qt5-uiplugin-5.12.2, qt5-webchannel-5.12.2, qt5-webengine-5.12.2, qt5-widgets-5.12.2, qt5-xml-5.12.2, qt5-xmlpatterns-5.12.2, qtchooser-66, re2-20190401, readline-8.0.0, shared-mime-info-1.10_1, snappy-1.1.6, sqlite3-3.28.0, suitesparse-5.2.0_3, tbb-2019.5, tcl86-8.6.9_1, tiff-4.0.10, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.2, x265-3.0_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-2.24_1, xmlcatmgr-2.2_2, xorg-fonts-truetype-7.7_1, xorgproto-2018.4, xprop-1.2.4, xset-1.2.4_2, xvid-1.3.5,1
Also listed in: Python

py36-orange3-single-cell-0.8.2_2
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_4, atk-2.28.1, avahi-app-0.7_2, binutils-2.32,1, blas-3.5.0_5, ca_root_nss-3.44, cairo-1.16.0,2, cblas-1.0_11, cups-2.2.11, dav1d-0.3.1, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.4_4,1, etc_os-release-0.1_2, expat-2.2.6_1, ffmpeg-4.1.3_6,1, fftw3-3.3.8_3, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, font-util-1.3.1, fontconfig-2.12.6,1, freeglut-3.0.0_2, freetype2-2.9.1, fribidi-0.19.7, gcc8-8.3.0_2, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, giflib-5.1.8, glib-2.56.3_5,1, gmake-4.2.1_3, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, graphviz-2.40.1_9, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.4.0_1, hdf-szip-2.1.1, hdf5-1.10.5_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_6, lapack-3.5.0_7, lcms-1.19_6,1, lcms2-2.9, libGLU-9.0.0_3, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXScrnSaver-1.2.3_2, libXau-1.0.9, libXaw-1.0.13_2,2, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXfontcache-1.0.5_5, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXmu-1.1.2_5,1, libXp-1.0.3_2,1, libXpm-3.5.12_2, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libedit-3.1.20181209_2,1, libepoll-shim-0.0.20190311, libevent-2.1.8_3, libffi-3.2.1_3, libfontenc-1.1.4, libgcrypt-1.8.4_1, libgd-2.2.5_1,1, libglade2-2.6.4_9, libgpg-error-1.36, libiconv-1.14_11, libidn2-2.1.1, libltdl-2.4.6, libmng-1.0.10_3, libogg-1.3.3,4, libpaper-1.1.24.4, libpci-3.6.2, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libtheora-1.1.1_7, libunistring-0.9.10_1, libunwind-20170615, libv4l-1.6.3_4, libva-2.4.1_1, libvdpau-1.1.1_2, libvorbis-1.3.6,3, libvpx-1.8.0, libx264-0.157.2945, libxcb-1.13.1, libxkbcommon-0.8.0_1, libxml2-2.9.8, libxshmfence-1.2_4, libxslt-1.1.32, llvm60-6.0.1_6, mesa-libs-18.3.2, metis-5.1.0_7, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.4.1_1, nspr-4.21, nss-3.44, openblas-0.2.20_8,1, opencv-core-3.4.1_17, openjpeg-2.3.1, openmp-8.0.0_1, opus-1.3.1, orange3-3.19.0_1, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, pcre2-10.32_1, perl5-5.28.2, pixman-0.34.0_1, png-1.6.37, py27-Babel-2.6.0_1, py27-Genesis-PyAPI-1.2.1, py27-SecretStorage-2.3.1, py27-astropy-1.1.2_2,1, py27-backports-1, py27-backports.functools_lru_cache-1.5, py27-bottleneck-1.2.1_4, py27-cffi-1.12.3, py27-dateutil-2.7.3, py27-dbus-1.2.8, py27-decorator-4.3.0, py27-docutils-0.14_4, py27-enum34-1.1.6, py27-gobject-2.28.6_8, py27-gtk2-2.24.0_5, py27-idna-2.8, py27-ipaddress-1.0.22, py27-joblib-0.13.0, py27-keyring-12.0.1_1, py27-keyrings.alt-3.1.1, py27-kiwisolver-1.1.0, py27-matplotlib-2.2.4, py27-numexpr-2.6.9, py27-numpy-1.16.1_2,1, py27-openssl-18.0.0, py27-pillow-5.3.0, py27-pycparser-2.18, py27-pyqtgraph-0.10.0_1, py27-pysocks-1.6.8, py27-pystemmer-1.3.0_2, py27-python-louvain-0.13_1, py27-pytz-2019.1,1, py27-qt5-gui-5.12.2, py27-qt5-printsupport-5.12.2, py27-qt5-widgets-5.12.2, py27-requests-2.21.0, py27-requests-cache-0.4.13, py27-scikit-learn-0.20.3, py27-scikit-sparse-0.4.4_2, py27-serverfiles-0.3.0, py27-sip-4.19.17,1, py27-six-1.12.0, py27-sphinx_rtd_theme-0.4.3, py27-sphinxcontrib-websupport-1.1.0, py27-urllib3-1.22,1, py35-setuptools-41.0.0, py36-AnyQt-0.0.10, py36-Jinja2-2.10, py36-MarkupSafe-1.1.1, py36-PyOpenGL-3.1.0_3, py36-alabaster-0.7.6, py36-asn1crypto-0.22.0, py36-cairo-1.14.1, py36-certifi-2019.3.9, py36-chardet-3.0.4_1, py36-cryptography-2.6.1, py36-cycler-0.10.0, py36-entrypoints-0.3, py36-fastTSNE-0.2.13_1, py36-fastdtw-0.3.2_1, py36-h5py-2.9.0_1, py36-imagesize-0.7.1, py36-llvmlite-0.25.0_2, py36-loompy-2.0.17, py36-networkx-2.1_1, py36-numba-0.40.1_4, py36-orange3-bioinformatics-3.2.2_2, py36-pandas-0.24.2, py36-pygments-2.3.0_1, py36-pygraphviz-1.3.1, py36-pyparsing-2.4.0, py36-qt5-core-5.12.2, py36-qt5-network-5.12.2, py36-qt5-qml-5.12.2, py36-qt5-webchannel-5.12.2, py36-qt5-webengine-5.12.1, py36-scipy-1.2.0_1, py36-slumber-0.7.1, py36-snowballstemmer-1.2.0_1, py36-sphinx-1.6.5_2,1, py36-sqlite3-3.6.8_7, py36-tkinter-3.6.8_6, py36-tornado-5.1.1, py36-xlrd-1.2.0_1, py36-yaml-5.1, pydbus-common-1.2.8, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, qscintilla2-qt5-2.11.1, qt5-assistant-5.12.2, qt5-concurrent-5.12.2, qt5-core-5.12.2_1, qt5-dbus-5.12.2, qt5-declarative-5.12.2, qt5-designer-5.12.2, qt5-gui-5.12.2, qt5-help-5.12.2, qt5-imageformats-5.12.2, qt5-location-5.12.2, qt5-network-5.12.2_1, qt5-printsupport-5.12.2, qt5-serialport-5.12.2, qt5-sql-5.12.2, qt5-sqldrivers-sqlite3-5.12.2, qt5-testlib-5.12.2, qt5-uiplugin-5.12.2, qt5-webchannel-5.12.2, qt5-webengine-5.12.2, qt5-widgets-5.12.2, qt5-xml-5.12.2, qt5-xmlpatterns-5.12.2, qtchooser-66, re2-20190401, readline-8.0.0, shared-mime-info-1.10_1, snappy-1.1.6, sqlite3-3.28.0, suitesparse-5.2.0_3, tbb-2019.5, tcl86-8.6.9_1, tiff-4.0.10, tk86-8.6.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.2, x265-3.0_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-2.24_1, xmlcatmgr-2.2_2, xorg-fonts-truetype-7.7_1, xorgproto-2018.4, xprop-1.2.4, xset-1.2.4_2, 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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py27-six-1.12.0, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0
Also listed in: Python

py36-pyfasta-0.5.2_3
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, blas-3.5.0_5, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-numpy-1.16.1_2,1, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, suitesparse-5.2.0_3
Also listed in: Python

py36-pysam-0.15.2
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, py35-cython-0.29_1, py35-setuptools-41.0.0, python35-3.5.7_2, python36-3.6.8_2, 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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.0.0, python35-3.5.7_2, python36-3.6.8_2, 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-0.19.8.1_2, indexinfo-0.3.1, libffi-3.2.1_3, py35-setuptools-41.0.0, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0
Also listed in: Python

pycogent-1.9_2
Toolkit for statistical analysis of biological sequences
Long description | Changes | Main Web Site
Maintained by: python@FreeBSD.org
Requires: binutils-2.32,1, blas-3.5.0_5, ca_root_nss-3.44, cblas-1.0_11, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, lapack-3.5.0_7, libffi-3.2.1_3, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, py27-Babel-2.6.0_1, py27-cffi-1.12.3, py27-docutils-0.14_4, py27-idna-2.8, py27-ipaddress-1.0.22, py27-numpy-1.16.1_2,1, py27-openssl-18.0.0, py27-pycparser-2.18, py27-pysocks-1.6.8, py27-pystemmer-1.3.0_2, py27-pytz-2019.1,1, py27-requests-2.21.0, py27-six-1.12.0, py27-sphinx_rtd_theme-0.4.3, py27-sphinxcontrib-websupport-1.1.0, py27-urllib3-1.22,1, py35-cython-0.29_1, py35-setuptools-41.0.0, py36-Jinja2-2.10, py36-MarkupSafe-1.1.1, py36-alabaster-0.7.6, py36-asn1crypto-0.22.0, py36-certifi-2019.3.9, py36-chardet-3.0.4_1, py36-cryptography-2.6.1, py36-imagesize-0.7.1, py36-pygments-2.3.0_1, py36-snowballstemmer-1.2.0_1, py36-sphinx-1.6.5_2,1, py36-sqlalchemy10-1.0.14, py36-sqlite3-3.6.8_7, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, sqlite3-3.28.0, suitesparse-5.2.0_3
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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1

raster3d-3.0.3_5
Set of tools for generating raster images of proteins and molecules
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: ImageMagick6-6.9.10.22_1,1, avahi-app-0.7_2, binutils-2.32,1, ca_root_nss-3.44, cairo-1.16.0,2, cups-2.2.11, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.4_4,1, expat-2.2.6_1, fftw3-3.3.8_3, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gcc8-8.3.0_2, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, ghostscript9-agpl-base-9.27_1, ghostscript9-agpl-x11-9.27, giflib-5.1.8, glib-2.56.3_5,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, harfbuzz-2.4.0_1, indexinfo-0.3.1, jbig2dec-0.16, jbigkit-2.1_1, jpeg-turbo-2.0.2, lcms2-2.9, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXxf86vm-1.1.4_3, libcroco-0.6.12, libdaemon-0.14_1, libdrm-2.4.96,1, 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, libidn2-2.1.1, liblqr-1-0.4.2, libltdl-2.4.6, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libraw-0.19.2, librsvg2-2.40.20, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libwmf-0.2.8.4_15, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, mesa-libs-18.3.2, mkfontscale-1.2.1, mpc-1.1.0_2, mpfr-4.0.2, nettle-3.4.1_1, openjpeg-2.3.1, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, perl5-5.28.2, pixman-0.34.0_1, pkgconf-1.6.1,1, png-1.6.37, poppler-data-0.4.9, python36-3.6.8_2, readline-8.0.0, shared-mime-info-1.10_1, tiff-4.0.10, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.2, xorg-fonts-truetype-7.7_1, xorgproto-2018.4
Also listed in: Graphics

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

rna-STAR-2.7.0.f
Spliced Transcripts Alignment to a Reference
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32,1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, gmp-6.1.2_1, indexinfo-0.3.1, mpc-1.1.0_2, mpfr-4.0.2

ruby25-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-3.1.20181209_2,1, libffi-3.2.1_3, libunwind-20170615, libyaml-0.2.2, ruby-2.5.5_2,1
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-3.1.20181209_2,1, libffi-3.2.1_3, libunwind-20170615, libyaml-0.2.2, ruby-2.5.5_2,1, ruby25-gems-3.0.3
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_2, autoconf-wrapper-20131203, automake-1.16.1_1, ca_root_nss-3.44, curl-7.64.1_1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, htslib-1.9, indexinfo-0.3.1, libnghttp2-1.38.0, m4-1.4.18_1,1, perl5-5.28.2

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, freetype2-2.9.1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, jpeg-turbo-2.0.2, libGLU-9.0.0_3, libX11-1.6.7,1, libXau-1.0.9, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, 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-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, mesa-libs-18.3.2, pciids-20190418, png-1.6.37, wayland-1.16.0_1, xorgproto-2018.4

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_6
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, boost-libs-1.70.0_2, ca_root_nss-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, icu-64.2,1, indexinfo-0.3.1, jsoncpp-1.8.1_6, libarchive-3.3.3,1, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libuv-1.29.0, lzo2-2.10_1, mpc-1.1.0_2, mpfr-4.0.2, ninja-1.9.0,2, python36-3.6.8_2, 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_3
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-3.44, cairo-1.16.0,2, cups-2.2.11, curl-7.64.1_1, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, encodings-1.0.4_4,1, 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, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gdbm-1.18.1_1, gdk-pixbuf2-2.36.12, gettext-runtime-0.19.8.1_2, gettext-tools-0.19.8.1_1, glib-2.56.3_5,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-2.4.0_1, hicolor-icon-theme-0.17, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-2.0.2, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXcomposite-0.4.4_5,1, libXcursor-1.1.15_2, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXft-2.3.2_3, libXi-1.7.9_2,1, libXinerama-1.1.4_2,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXxf86vm-1.1.4_3, libdaemon-0.14_1, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, libfontenc-1.1.4, libiconv-1.14_11, libidn2-2.1.1, libnghttp2-1.38.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libunistring-0.9.10_1, libunwind-20170615, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, mesa-libs-18.3.2, mkfontscale-1.2.1, nettle-3.4.1_1, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, pixman-0.34.0_1, pkgconf-1.6.1,1, png-1.6.37, python36-3.6.8_2, readline-8.0.0, shared-mime-info-1.10_1, sqlite3-3.28.0, tiff-4.0.10, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, xorg-fonts-truetype-7.7_1, xorgproto-2018.4

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_2
Multibody dynamics library for (bio)mechanical systems simulation
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.32,1, ca_root_nss-3.44, cmake-3.14.4, curl-7.64.1_1, expat-2.2.6_1, freeglut-3.0.0_2, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, indexinfo-0.3.1, jsoncpp-1.8.1_6, libGLU-9.0.0_3, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXmu-1.1.2_5,1, libXrandr-1.5.1_2, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXxf86vm-1.1.4_3, libarchive-3.3.3,1, libdrm-2.4.96,1, libepoll-shim-0.0.20190311, libffi-3.2.1_3, liblz4-1.9.1,1, libnghttp2-1.38.0, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libuv-1.29.0, libxcb-1.13.1, libxml2-2.9.8, libxshmfence-1.2_4, lzo2-2.10_1, mesa-libs-18.3.2, mpc-1.1.0_2, mpfr-4.0.2, openblas-0.2.20_8,1, pciids-20190418, rhash-1.3.5, wayland-1.16.0_1, xorgproto-2018.4
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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1

stacks-2.4
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, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, 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, python36-3.6.8_2, 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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1

tRNAscan-SE-2.0.0_1
Searching for tRNA genes in genomic sequence
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: autoconf-2.69_2, autoconf-wrapper-20131203, automake-1.16.1_1, indexinfo-0.3.1, infernal-1.1.2, m4-1.4.18_1,1, perl5-5.28.2

t_coffee-9.03_10
Multiple DNA or protein sequence alignment package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.32,1, clustalw-2.1_2, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, 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-3.44, curl-7.64.1_1, htslib-1.9, libnghttp2-1.38.0

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-0.35
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, freetype2-2.9.1, giflib-5.1.8, java-zoneinfo-2019.a, javavmwrapper-2.6, libICE-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXi-1.7.9_2,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, libXtst-1.2.3_2, libfontenc-1.1.4, libinotify-20180201_1, libpthread-stubs-0.4, libxcb-1.13.1, libxml2-2.9.8, mkfontscale-1.2.1, openjdk8-8.212.4.1, xorgproto-2018.4
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-5.0.7, ca_root_nss-3.44, cairo-1.16.0,2, cups-2.2.11, dav1d-0.3.1, dbus-1.12.12, dbus-glib-0.110, dejavu-2.37_1, desktop-file-utils-0.23, encodings-1.0.4_4,1, etc_os-release-0.1_2, expat-2.2.6_1, ffmpeg-4.1.3_6,1, font-bh-ttf-1.0.3_4, font-misc-ethiopic-1.0.3_4, font-misc-meltho-1.0.3_4, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gdbm-1.18.1_1, gettext-runtime-0.19.8.1_2, giflib-5.1.8, glib-2.56.3_5,1, gmp-6.1.2_1, gnome_subr-1.0, gnutls-3.6.7, gobject-introspection-1.56.1,1, graphite2-1.3.13, gstreamer1-1.14.4, gstreamer1-libav-1.14.4_2, gstreamer1-plugins-1.14.4_1, 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-2.4.0_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-1.0.9_3,1, libSM-1.2.3,1, libX11-1.6.7,1, libXau-1.0.9, libXcomposite-0.4.4_5,1, libXdamage-1.1.4_5, libXdmcp-1.1.3, libXext-1.3.3_3,1, libXfixes-5.0.3_2, libXfontcache-1.0.5_5, libXft-2.3.2_3, libXi-1.7.9_2,1, libXmu-1.1.2_5,1, libXrender-0.9.10_2, libXt-1.1.5_2,1, 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-2.4.96,1, 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-1.8.4_1, libgpg-error-1.36, libiconv-1.14_11, libidn2-2.1.1, libltdl-2.4.6, libmng-1.0.10_3, libogg-1.3.3,4, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13_1, libtheora-1.1.1_7, libunistring-0.9.10_1, libunwind-20170615, libv4l-1.6.3_4, libva-2.4.1_1, libvdpau-1.1.1_2, libvorbis-1.3.6,3, libvpx-1.8.0, libx264-0.157.2945, libxcb-1.13.1, libxkbcommon-0.8.0_1, libxml2-2.9.8, libxshmfence-1.2_4, libxslt-1.1.32, mesa-libs-18.3.2, mkfontscale-1.2.1, mpg123-1.25.10, nettle-3.4.1_1, opencv-core-3.4.1_17, opus-1.3.1, orc-0.4.28, p11-kit-0.23.15, pango-1.42.4_2, pciids-20190418, pcre-8.43_1, pcre2-10.32_1, perl5-5.28.2, pixman-0.34.0_1, png-1.6.37, python36-3.6.8_2, qt5-buildtools-5.12.2, qt5-concurrent-5.12.2, qt5-core-5.12.2_1, qt5-dbus-5.12.2, qt5-declarative-5.12.2, qt5-gui-5.12.2, qt5-imageformats-5.12.2, qt5-linguisttools-5.12.2, qt5-location-5.12.2, qt5-network-5.12.2_1, qt5-opengl-5.12.2, qt5-printsupport-5.12.2, qt5-qmake-5.12.2, qt5-script-5.12.2, qt5-scripttools-5.12.2, qt5-sensors-5.12.2, qt5-serialport-5.12.2, qt5-sql-5.12.2, qt5-svg-5.12.2, qt5-testlib-5.12.2, qt5-webchannel-5.12.2, qt5-webkit-5.212.0.a2_21, qt5-widgets-5.12.2, qt5-xml-5.12.2, qt5-xmlpatterns-5.12.2, qtchooser-66, readline-8.0.0, shared-mime-info-1.10_1, sqlite3-3.28.0, tiff-4.0.10, tpm-emulator-0.7.4_2, trousers-0.3.14_2, wayland-1.16.0_1, webp-1.0.2, x265-3.0_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-2.24_1, xorg-fonts-truetype-7.7_1, xorgproto-2018.4, xprop-1.2.4, xset-1.2.4_2, xvid-1.3.5,1
Also listed in: Science

unanimity-3.4.1_1
Pacific Biosciences consensus library and applications
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.32,1, blas-3.5.0_5, boost-libs-1.70.0_2, ca_root_nss-3.44, cblas-1.0_11, curl-7.64.1_1, gcc8-8.3.0_2, gettext-runtime-0.19.8.1_2, gmp-6.1.2_1, htslib-1.9, icu-64.2,1, indexinfo-0.3.1, lapack-3.5.0_7, libedit-3.1.20181209_2,1, libffi-3.2.1_3, libnghttp2-1.38.0, lua52-5.2.4, meson-0.50.0, metis-5.1.0_7, mpc-1.1.0_2, mpfr-4.0.2, ninja-1.9.0,2, openblas-0.2.20_8,1, pbbam-0.18.0_1, pbcopper-0.4.1_1, pcre-8.43_1, pkgconf-1.6.1,1, py27-numpy-1.16.1_2,1, py35-setuptools-41.0.0, python27-2.7.16_1, python35-3.5.7_2, python36-3.6.8_2, readline-8.0.0, seqan-2.4.0, suitesparse-5.2.0_3, 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-3.44, curl-7.64.1_1, fastahack-g20160702, filevercmp-g20151117, fsom-g20151117_1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, htslib-1.9, indexinfo-0.3.1, intervaltree-g20151213_1, libffi-3.2.1_3, libnghttp2-1.38.0, multichoose-1.0.3.2, python36-3.6.8_2, 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_2, autoconf-wrapper-20131203, automake-1.16.1_1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, m4-1.4.18_1,1, perl5-5.28.2, pkgconf-1.6.1,1

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-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libffi-3.2.1_3, perl5-5.28.2, python36-3.6.8_2, readline-8.0.0

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_2, autoconf-wrapper-20131203, automake-1.16.1_1, gettext-runtime-0.19.8.1_2, gmake-4.2.1_3, indexinfo-0.3.1, libsysinfo-0.0.3_2, m4-1.4.18_1,1, perl5-5.28.2

wise-2.4.1_1
Intelligent algorithms for DNA searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_2, glib-2.56.3_5,1, indexinfo-0.3.1, libffi-3.2.1_3, libiconv-1.14_11, libxml2-2.9.8, pcre-8.43_1, pkgconf-1.6.1,1, python36-3.6.8_2, readline-8.0.0

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