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FreeBSD Ports: Biology

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Software related to biology.

FastTree-2.1.10_1
Approximately-maximum-likelihood phylogenetic trees from alignments
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.30_3,1, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, mpc-1.1.0_1, mpfr-4.0.1

InsightToolkit-4.13.0_2
Insight Toolkit
Long description | Changes | Main Web Site
Maintained by: woodsb02@FreeBSD.org
Requires: binutils-2.30_3,1, ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, fftw-2.1.5_16, gcc-ecj-4.5, gcc6-6.4.0_7, gdcm-2.6.3_2, gettext-runtime-0.19.8.1_1, gmp-6.1.2, googletest-1.8.0.712, hdf-szip-2.1_2, hdf5-1.10.1_1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, jsoncpp-1.8.1_3, lcms2-2.9, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, mpc-1.1.0_1, mpfr-4.0.1, ninja-1.8.2,2, openjpeg15-1.5.2_1, png-1.6.34, python27-2.7.15, readline-7.0.3_1, rhash-1.3.5, tiff-4.0.9_1
Also listed in: Science

MOOSE-neural-simulator-3.1.2_1
Multiphysics Object Oriented Simulation Environment
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: avahi-app-0.6.31_6, bash-4.4.23, binutils-2.30_3,1, blas-3.5.0_4, ca_root_nss-3.37.3, cairo-1.14.8_1,2, cblas-1.0_8, cmake-3.11.3, cups-2.2.8_1, curl-7.60.0, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontcacheproto-0.1.3, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gcc-ecj-4.5, gcc6-6.4.0_7, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, graphviz-2.40.1_5, gsl-2.4, gstreamer-0.10.36_6, gstreamer-plugins-0.10.36_8,3, harfbuzz-1.8.1, hdf-szip-2.1_2, hdf5-1.10.1_1, hicolor-icon-theme-0.15, icu-61.1,1, indexinfo-0.3.1, inputproto-2.3.2, jbigkit-2.1_1, jpeg-turbo-1.5.3, jsoncpp-1.8.1_3, kbproto-1.0.7, lapack-3.5.0_4, lcms-1.19_6,1, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXScrnSaver-1.2.2_3, libXau-1.0.8_3, libXaw-1.0.13,2, libXcursor-1.1.15, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXfontcache-1.0.5_3, libXft-2.3.2_1, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXv-1.0.11,1, libXxf86vm-1.1.4_1, libarchive-3.3.2,1, libdaemon-0.14_1, libdrm-2.4.92,1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libidn2-2.0.5, libltdl-2.4.6, liblz4-1.8.2,1, libmng-1.0.10_3, libnghttp2-1.32.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libsbml-5.16.0, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libuv-1.20.3, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, lzo2-2.10_1, mesa-libs-18.1.2, metis-5.1.0_4, mkfontdir-1.0.7, mkfontscale-1.1.3, mpc-1.1.0_1, mpfr-4.0.1, nettle-3.4, openblas-0.2.20_2,1, orc-0.4.25, p11-kit-0.23.12, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, png-1.6.34, printproto-1.0.5, py27-cycler-0.10.0, py27-decorator-4.3.0, py27-pyparsing-2.2.0, py27-pytz-2018.4,1, py27-scipy-1.1.0, py27-suds-jurko-0.6, py27-yaml-3.12, py34-numpy-1.14.3,1, py35-tkinter-3.5.5_6, py36-dateutil-2.6.1, py36-matplotlib-2.1.2_2, py36-networkx-1.10_4, py36-pygraphviz-1.3.1, py36-qt4-core-4.12.1_7,1, py36-qt4-gui-4.12.1_3,1, py36-qt4-test-4.12.1_3,1, py36-scikit-sparse-0.4.3_1, py36-setuptools-39.2.0, py36-sip-4.19.8,1, py36-six-1.11.0, py36-tornado-5.0.2, python27-2.7.15, python34-3.4.8, python35-3.5.5, python36-3.6.5, qscintilla2-2.10.4,1, qt4-assistant-4.8.7_1, qt4-clucene-4.8.7_2, qt4-corelib-4.8.7_12, qt4-declarative-4.8.7_1, qt4-designer-4.8.7_1, qt4-doc-4.8.7_1, qt4-gui-4.8.7_3, qt4-help-4.8.7_2, qt4-iconengines-4.8.7_2, qt4-imageformats-4.8.7_2, qt4-inputmethods-4.8.7_2, qt4-network-4.8.7_3, qt4-opengl-4.8.7_3, qt4-qt3support-4.8.7_2, qt4-script-4.8.7_3, qt4-sql-4.8.7_2, qt4-sqlite-plugin-4.8.7_4, qt4-svg-4.8.7_2, qt4-testlib-4.8.7_2, qt4-webkit-4.8.7_3, qt4-xml-4.8.7_2, qt4-xmlpatterns-4.8.7_2, qtchooser-39, randrproto-1.5.0, readline-7.0.3_1, renderproto-0.11.1, rhash-1.3.5, scrnsaverproto-1.2.2, sqlite3-3.24.0, suitesparse-5.2.0, tcl86-8.6.8, tiff-4.0.9_1, tk86-8.6.8_2, tpm-emulator-0.7.4_2, trousers-0.3.14_2, videoproto-2.3.3, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xdg-utils-1.1.1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xprop-1.2.3, xproto-7.0.31, xset-1.2.4
Also listed in: Science

afni-2015.11.13_6
Advanced Functional Neuro Imaging
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: R-3.5.0, avahi-app-0.6.31_6, binutils-2.30_3,1, ca_root_nss-3.37.3, cairo-1.14.8_1,2, cups-2.2.8_1, curl-7.60.0, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, dri3proto-1.0, encodings-1.0.4_4,1, endian-1.1, expat-2.2.5, f2c-20060810_6, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gcc-ecj-4.5, gcc6-6.4.0_7, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, gettext-tools-0.19.8.1, ghostscript9-agpl-base-9.23, glib-2.50.3_3,1, glproto-1.4.17, gmake-4.2.1_2, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, gsl-2.4, harfbuzz-1.8.1, hdf-szip-2.1_2, hdf5-1.10.1_1, icu-61.1,1, indexinfo-0.3.1, inputproto-2.3.2, jasper-1.900.1_17, jbig2dec-0.14, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, lcms2-2.9, libGLU-9.0.0_3, libGLw-8.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXScrnSaver-1.2.2_3, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.92,1, libffi-3.2.1_2, libfontenc-1.1.3_1, libiconv-1.14_11, libidn-1.34, libidn2-2.0.5, libijs-0.35_5, libnghttp2-1.32.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, m4-1.4.18,1, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mpc-1.1.0_1, mpeg_encode-1.5b, mpfr-4.0.1, netcdf-4.6.1, netcdf-fortran-4.4.4_5, netpbm-10.80.00, nettle-3.4, open-motif-2.3.8, openjpeg-2.3.0, openmp-6.0.0, p11-kit-0.23.12, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, poppler-data-0.4.9, printproto-1.0.5, python27-2.7.15, qhull5-1.0_3, readline-7.0.3_1, renderproto-0.11.1, scrnsaverproto-1.2.2, tcl86-8.6.8, tiff-4.0.9_1, tk86-8.6.8_2, tpm-emulator-0.7.4_2, trousers-0.3.14_2, xbitmaps-1.1.2, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
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_1, bash-4.4.23, dejavu-2.37, expat-2.2.5, fixesproto-5.0, fontconfig-2.12.6,1, freetype2-2.9.1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, gmake-4.2.1_2, indexinfo-0.3.1, inputproto-2.3.2, java-zoneinfo-2018.e, javavmwrapper-2.6, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, mkfontdir-1.0.7, mkfontscale-1.1.3, openjdk8-8.172.11, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.31
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-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.15, readline-7.0.3_1, 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-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.15, readline-7.0.3_1, rhash-1.3.5

bcftools-1.6
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.16.1, ca_root_nss-3.37.3, curl-7.60.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, gsl-2.4, htslib-1.6, indexinfo-0.3.1, libnghttp2-1.32.0, m4-1.4.18,1, perl5-5.26.2

bedtools-2.27.1_1
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_1, gmake-4.2.1_2, indexinfo-0.3.1, libffi-3.2.1_2, python27-2.7.15, readline-7.0.3_1

biococoa-2.2.2_4
Bioinformatics framework
Long description | Changes | Main Web Site
Maintained by: theraven@FreeBSD.org
Requires: avahi-app-0.6.31_6, ca_root_nss-3.37.3, cairo-1.14.8_1,2, cups-2.2.8_1, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dri2proto-2.8, expat-2.2.5, fixesproto-5.0, flac-1.3.2, flite-1.4_2, fontconfig-2.12.6,1, freetype2-2.9.1, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, gmake-4.2.1_2, gmp-6.1.2, gnome_subr-1.0, gnustep-back-0.25.1_1, gnustep-base-1.25.0_4, gnustep-gui-0.25.1_4, gnustep-make-2.7.0_1, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, icu-61.1,1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libGLU-9.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcursor-1.1.15, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libao-1.2.0_3, libdaemon-0.14_1, libdrm-2.4.92,1, libffi-3.2.1_2, libgcrypt-1.8.3, libgpg-error-1.31, libiconv-1.14_11, libidn2-2.0.5, libobjc2-1.8.1, libogg-1.3.3,4, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libsndfile-1.0.28_1, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libvorbis-1.3.6,3, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, libxslt-1.1.32, mesa-libs-18.1.2, nettle-3.4, p11-kit-0.23.12, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, png-1.6.34, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, tiff-4.0.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.31
Also listed in: Gnustep

blat-36
Fast tool for local sequence similarity searches
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, libedit-3.1.20170329_2,1, libevent-2.1.8_1, liblz4-1.8.2,1, mysql56-client-5.6.40, perl5-5.26.2, png-1.6.34

bowtie-1.1.2_5
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.30_3,1, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, gmp-6.1.2, indexinfo-0.3.1, libffi-3.2.1_2, mpc-1.1.0_1, mpfr-4.0.1, perl5-5.26.2, python27-2.7.15, readline-7.0.3_1

bowtie2-2.3.3.1
Ultrafast, memory-efficient short read aligner
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, libffi-3.2.1_2, perl5-5.26.2, python27-2.7.15, readline-7.0.3_1, tbb-2018.2

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_1, gmake-4.2.1_2, indexinfo-0.3.1, perl5-5.26.2

canu-1.7
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_1, atk-2.24.0, avahi-app-0.6.31_6, binutils-2.30_3,1, boost-libs-1.67.0_1, ca_root_nss-3.37.3, cairo-1.14.8_1,2, compositeproto-0.4.2, cups-2.2.8_1, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dconf-0.26.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gcc-ecj-4.5, gcc6-6.4.0_7, gconf2-3.2.6_5, gdbm-1.13_1, gdk-pixbuf2-2.36.11, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, gmake-4.2.1_2, gmp-6.1.2, gnome_subr-1.0, gnuplot-5.2.4, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, gstreamer-0.10.36_6, gstreamer-plugins-0.10.36_8,3, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-1.8.1, hicolor-icon-theme-0.15, icu-61.1,1, indexinfo-0.3.1, inputproto-2.3.2, jasper-1.900.1_17, java-zoneinfo-2018.e, javavmwrapper-2.6, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libGLU-9.0.0_3, libICE-1.0.9_1,1, libIDL-0.8.14_3, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.15, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libXv-1.0.11,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libidn2-2.0.5, libmspack-0.5, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, lua53-5.3.4_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mpc-1.1.0_1, mpfr-4.0.1, nettle-3.4, nspr-4.19, openjdk8-8.172.11, orc-0.4.25, p11-kit-0.23.12, pango-1.42.0, pangox-compat-0.0.2_2, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, png-1.6.34, polkit-0.114, python27-2.7.15, randrproto-1.5.0, readline-7.0.3_1, recordproto-1.14.2, renderproto-0.11.1, shared-mime-info-1.8, spidermonkey52-52.8.0, tex-kpathsea-6.2.1_1, tiff-4.0.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, videoproto-2.3.3, webp-1.0.0, wx28-gtk2-2.8.12_7, wx28-gtk2-common-2.8.12_7, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Java, Perl5

cd-hit-4.6.6_3
Clustering and comparing protein or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.30_3,1, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, gmp-6.1.2, indexinfo-0.3.1, mpc-1.1.0_1, mpfr-4.0.1

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_1, gmake-4.2.1_2, indexinfo-0.3.1

chemeq-1.50_2
Outputs LaTeX code for chemical reaction
Long description | Changes
Maintained by: ports@FreeBSD.org
Requires: bison-3.0.4,1, gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, m4-1.4.18,1
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

clustalx-2.1
Multiple alignment of nucleic acid and protein sequences with GUI
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: avahi-app-0.6.31_6, ca_root_nss-3.37.3, cups-2.2.8_1, dbus-1.10.16_1, dbus-glib-0.108, expat-2.2.5, fixesproto-5.0, fontcacheproto-0.1.3, fontconfig-2.12.6,1, freetype2-2.9.1, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, glib-2.50.3_3,1, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, hicolor-icon-theme-0.15, icu-61.1,1, indexinfo-0.3.1, inputproto-2.3.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcursor-1.1.15, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXfontcache-1.0.5_3, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXmu-1.1.2_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libdaemon-0.14_1, libffi-3.2.1_2, libiconv-1.14_11, libidn2-2.0.5, libpaper-1.1.24.4, libpthread-stubs-0.4, libtasn1-4.13, libunistring-0.9.10, libxcb-1.13, libxml2-2.9.7, nettle-3.4, p11-kit-0.23.12, pcre-8.42, perl5-5.26.2, png-1.6.34, python27-2.7.15, qt4-corelib-4.8.7_12, qt4-gui-4.8.7_3, qt4-moc-4.8.7_2, qt4-qmake-4.8.7_2, qt4-xml-4.8.7_2, qtchooser-39, randrproto-1.5.0, readline-7.0.3_1, renderproto-0.11.1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, xdg-utils-1.1.1, xextproto-7.3.0, xineramaproto-1.2.1, xprop-1.2.3, xproto-7.0.31, xset-1.2.4

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-c6-6.9_7, perl5-5.26.2, phrap-1.090518, phred-0.020425.c

cycle-0.3.1_10
Calendar program for women
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ORBit2-2.14.19_2, atk-2.24.0, avahi-app-0.6.31_6, ca_root_nss-3.37.3, cairo-1.14.8_1,2, cantarell-fonts-0.0.25, compositeproto-0.4.2, cups-2.2.8_1, curl-7.60.0, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dconf-0.26.1, dejavu-2.37, dri2proto-2.8, enchant-1.6.0_8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gconf2-3.2.6_5, gdbm-1.13_1, gdk-pixbuf2-2.36.11, geoclue-2.4.3, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glib-networking-2.50.0, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, gsettings-desktop-schemas-3.18.1, gstreamer1-1.12.3, gstreamer1-plugins-1.12.3, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-1.8.1, harfbuzz-icu-1.8.1_1, hicolor-icon-theme-0.15, hunspell-1.6.2, icu-61.1,1, indexinfo-0.3.1, inputproto-2.3.2, iso-codes-3.76, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.3, json-glib-1.2.8, kbproto-1.0.7, libGLU-9.0.0_3, libICE-1.0.9_1,1, libIDL-0.8.14_3, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.15, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.92,1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgcrypt-1.8.3, libgpg-error-1.31, libiconv-1.14_11, libidn2-2.0.5, libmspack-0.5, libnghttp2-1.32.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libproxy-0.4.12, libpthread-stubs-0.4, libsecret-0.18.6, libsoup-2.54.1, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, libxslt-1.1.32, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, nettle-3.4, nspr-4.19, orc-0.4.25, p11-kit-0.23.12, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, png-1.6.34, polkit-0.114, py27-wxPython-common-3.0.2.0_4, py27-wxPython30-3.0.2.0_4, py36-setuptools-39.2.0, python27-2.7.15, python36-3.6.5, randrproto-1.5.0, readline-7.0.3_1, renderproto-0.11.1, shared-mime-info-1.8, spidermonkey52-52.8.0, sqlite3-3.24.0, tiff-4.0.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, webkit-gtk2-2.4.11_15, webp-1.0.0, wx30-gtk2-3.0.3.1, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Deskutils, Python

dDocent-2.2.25
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_1, atk-2.24.0, avahi-app-0.6.31_6, bamtools-2.5.1, bash-4.4.23, bedtools-2.27.1_1, binutils-2.30_3,1, bwa-0.7.17, ca_root_nss-3.37.3, cairo-1.14.8_1,2, cd-hit-4.6.6_3, compositeproto-0.4.2, coreutils-8.28, cups-2.2.8_1, curl-7.60.0, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dconf-0.26.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fastahack-g20160702, filevercmp-g20151117, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freebayes-1.2.0, freetype2-2.9.1, fribidi-0.19.7, fsom-g20151117, gawk-4.1.4_2, gcc-ecj-4.5, gcc6-6.4.0_7, gconf2-3.2.6_5, gdbm-1.13_1, gdk-pixbuf2-2.36.11, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnuplot-5.2.4, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, gstreamer-0.10.36_6, gstreamer-plugins-0.10.36_8,3, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-1.8.1, hicolor-icon-theme-0.15, htslib-1.6, icu-61.1,1, indexinfo-0.3.1, inputproto-2.3.2, intervaltree-g20151213, jasper-1.900.1_17, java-zoneinfo-2018.e, javavmwrapper-2.6, jbigkit-2.1_1, jpeg-turbo-1.5.3, jsoncpp-1.8.1_3, kbproto-1.0.7, libGLU-9.0.0_3, libICE-1.0.9_1,1, libIDL-0.8.14_3, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.15, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libXv-1.0.11,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libidn2-2.0.5, libmspack-0.5, libnghttp2-1.32.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libsigsegv-2.12, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, lua53-5.3.4_2, mawk-1.3.4.20161120, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mpc-1.1.0_1, mpfr-4.0.1, multichoose-1.0.3.2, nettle-3.4, nspr-4.19, openjdk8-8.172.11, orc-0.4.25, p11-kit-0.23.12, pango-1.42.0, pangox-compat-0.0.2_2, parallel-20171222, pciids-20180428, pcre-8.42, pear-merger-0.9.6, perl5-5.26.2, pixman-0.34.0, png-1.6.34, polkit-0.114, python27-2.7.15, rainbow-2.0.4, randrproto-1.5.0, readline-7.0.3_1, recordproto-1.14.2, renderproto-0.11.1, samtools-1.6, seqtk-1.2.8, shared-mime-info-1.8, smithwaterman-g20160702, spidermonkey52-52.8.0, stacks-1.48, tabixpp-1.0.0.10, tex-kpathsea-6.2.1_1, tiff-4.0.9_1, 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-0.1.15, videoproto-2.3.3, webp-1.0.0, wx28-gtk2-2.8.12_7, wx28-gtk2-common-2.8.12_7, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Java

diamond-0.9.22
BLAST-compatible local sequence aligner
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.15, readline-7.0.3_1, rhash-1.3.5

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-2.2.5, fontconfig-2.12.6,1, freetype2-2.9.1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, gmake-4.2.1_2, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libgd-2.2.4_1,1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, open-motif-2.3.8, png-1.6.34, primer3-2.3.6, printproto-1.0.5, renderproto-0.11.1, tiff-4.0.9_1, webp-1.0.0, xbitmaps-1.1.2, xextproto-7.3.0, xproto-7.0.31

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

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_1, dejavu-2.37, expat-2.2.5, fixesproto-5.0, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.4, inputproto-2.3.2, java-zoneinfo-2018.e, javavmwrapper-2.6, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, mkfontdir-1.0.7, mkfontscale-1.1.3, openjdk8-8.172.11, perl5-5.26.2, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.31
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_1, autoconf-wrapper-20131203, automake-1.16.1, indexinfo-0.3.1, libgtextutils-0.7, libtool-2.4.6, m4-1.4.18,1, perl5-5.26.2, pkgconf-1.4.2,1

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

freebayes-1.2.0
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_1, gmake-4.2.1_2, 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_1, gmake-4.2.1_2, indexinfo-0.3.1, kbproto-1.0.7, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, xproto-7.0.31

gff2ps-0.98d_2
Converts gff-formated genomic data-sets to PostScript
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: bash-4.4.23, gawk-4.1.4_2, gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, libsigsegv-2.12, readline-7.0.3_1

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_1, gmake-4.2.1_2, indexinfo-0.3.1, perl5-5.26.2

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-2.24.0, avahi-app-0.6.31_6, ca_root_nss-3.37.3, cairo-1.14.8_1,2, compositeproto-0.4.2, cups-2.2.8_1, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gdbm-1.13_1, gdk-pixbuf2-2.36.11, gettext-runtime-0.19.8.1_1, gettext-tools-0.19.8.1, glib-2.50.3_3,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-1.8.1, hicolor-icon-theme-0.15, indexinfo-0.3.1, inputproto-2.3.2, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.15, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.92,1, libffi-3.2.1_2, libfontenc-1.1.3_1, libiconv-1.14_11, libidn2-2.0.5, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, nettle-3.4, p11-kit-0.23.12, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, python27-2.7.15, randrproto-1.5.0, readline-7.0.3_1, renderproto-0.11.1, shared-mime-info-1.8, tiff-4.0.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31

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_1, gmake-4.2.1_2, indexinfo-0.3.1

hmmer-3.1b2
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_1, gmake-4.2.1_2, indexinfo-0.3.1

htslib-1.6
C library for high-throughput sequencing data formats
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.16.1, ca_root_nss-3.37.3, curl-7.60.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, libnghttp2-1.32.0, m4-1.4.18,1, perl5-5.26.2
Also listed in: Devel

hyphy-2.3.13
Hypothesis testing using Phylogenies
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.15, readline-7.0.3_1, rhash-1.3.5

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_1, gmake-4.2.1_2, indexinfo-0.3.1

io_lib-1.14.9
General purpose trace file (and Experiment File) reading interface
Long description | Changes | Main Web Site
Maintained by: danilo@FreeBSD.org
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.16.1, ca_root_nss-3.37.3, curl-7.60.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, libnghttp2-1.32.0, libtool-2.4.6, m4-1.4.18,1, perl5-5.26.2

iqtree-1.6.5
Efficient phylogenomic software by maximum likelihood
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.30_3,1, ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, eigen-3.3.4, expat-2.2.5, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, mpc-1.1.0_1, mpfr-4.0.1, ninja-1.8.2,2, python27-2.7.15, readline-7.0.3_1, 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_1, apache-ant-1.10.3, dejavu-2.37, expat-2.2.5, fixesproto-5.0, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.4, inputproto-2.3.2, java-zoneinfo-2018.e, javavmwrapper-2.6, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, mkfontdir-1.0.7, mkfontscale-1.1.3, openjdk8-8.172.11, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.31
Also listed in: Java

jellyfish-2.2.6_2
Fast, memory-efficient counting of k-mers in DNA
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.16.1, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, libedit-3.1.20170329_2,1, libffi-3.2.1_2, libtool-2.4.6, libunwind-20170615, libyaml-0.1.6_2, m4-1.4.18,1, perl5-5.26.2, pkgconf-1.4.2,1, ruby-2.4.4,1, yaggo-1.5.9

kallisto-0.43.1
Quantify abundances of transcripts from RNA-Seq data
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gettext-runtime-0.19.8.1_1, hdf-szip-2.1_2, hdf5-1.10.1_1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.15, readline-7.0.3_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: perl5-5.26.2

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_1, autoconf-wrapper-20131203, automake-1.16.1, indexinfo-0.3.1, libtool-2.4.6, m4-1.4.18,1, perl5-5.26.2, pkgconf-1.4.2,1

libsbml-5.16.0
API Library for Working with SBML File
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, libxml2-2.9.7, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.15, readline-7.0.3_1, 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: onatan@gmail.com
Requires: linux_base-c6-6.9_7

mafft-7.266
Multiple alignment program for amino acid or nucleotide sequences
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, 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_6
Medical Imaging NetCDF
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.16.1, bash-4.4.23, bison-3.0.4,1, ca_root_nss-3.37.3, curl-7.60.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, hdf-szip-2.1_2, hdf5-1.10.1_1, indexinfo-0.3.1, libnghttp2-1.32.0, libtool-2.4.6, m4-1.4.18,1, netcdf-4.6.1, perl5-5.26.2, pkgconf-1.4.2,1
Also listed in: Science

molden-5.7_15
Display molecular orbitals and electron densities in 2D and 3D
Long description | Changes | Main Web Site
Maintained by: jmd@FreeBSD.org
Requires: binutils-2.30_3,1, damageproto-1.2.1, dri2proto-2.8, dri3proto-1.0, expat-2.2.5, fixesproto-5.0, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, glproto-1.4.17, gmake-4.2.1_2, gmp-6.1.2, indexinfo-0.3.1, kbproto-1.0.7, libGLU-9.0.0_3, libX11-1.6.5,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mpc-1.1.0_1, mpfr-4.0.1, pciids-20180428, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.31

mopac-7.1.15_4
Semi-empirical (MNDO, etc.) molecular orbital calculation
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.30_3,1, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, gmp-6.1.2, indexinfo-0.3.1, mpc-1.1.0_1, mpfr-4.0.1

mrbayes-3.1.2_2
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_1, gmake-4.2.1_2, indexinfo-0.3.1, readline-7.0.3_1

mummer-3.23_2
Modular system for rapid whole genome alignment
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, perl5-5.26.2

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-2.7.1
NCBI implementation of Basic Local Alignment Search Tool
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.30_3,1, ca_root_nss-3.37.3, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, gmp-6.1.2, gnutls-3.5.18, indexinfo-0.3.1, libffi-3.2.1_2, libgcrypt-1.8.3, libgpg-error-1.31, libidn2-2.0.5, libtasn1-4.13, libunistring-0.9.10, lmdb-0.9.22,1, lzo2-2.10_1, mpc-1.1.0_1, mpfr-4.0.1, nettle-3.4, p11-kit-0.23.12, p5-Exporter-Tiny-1.000000, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, pcre-8.42, perl5-5.26.2, python27-2.7.15, readline-7.0.3_1, sqlite3-3.24.0, tpm-emulator-0.7.4_2, trousers-0.3.14_2
Also listed in: Perl5, Python

ncbi-toolkit-2012.06.20_1
NCBI development toolkit, including BLAST 2 and GenBank/Entrez support
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: expat-2.2.5, fontconfig-2.12.6,1, freetype2-2.9.1, gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, open-motif-2.3.8, png-1.6.34, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.2, xextproto-7.3.0, xproto-7.0.31

ngs-sdk-2.9.0
Tools and libraries for using data in the INSDC Sequence Read Archives
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, perl5-5.26.2

njplot-2.4
Phylogenetic tree drawing program
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: expat-2.2.5, fontconfig-2.12.6,1, freetype2-2.9.1, gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, ncbi-toolkit-2012.06.20_1, open-motif-2.3.8, png-1.6.34, printproto-1.0.5, renderproto-0.11.1, xbitmaps-1.1.2, xextproto-7.3.0, xproto-7.0.31

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-0.17026, p5-File-NFSLock-1.21_1, p5-Heap-0.80_1, p5-IO-String-1.08_1, p5-IPC-ShareLite-0.17_1, p5-TimeDate-2.30_2,1, perl5-5.26.2
Also listed in: Databases, Perl5

p5-Bio-ASN1-EntrezGene-1.72_1
Regular expression-based Perl Parser for NCBI Entrez Gene
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, graphite2-1.3.11, graphviz-2.40.1_5, harfbuzz-1.8.1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libevent-2.1.8_1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.2,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mysql56-client-5.6.40, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.1, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007002, p5-CGI-4.38, p5-Class-Method-Modifiers-2.12, p5-Clone-0.39, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.046, p5-DBI-1.641, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17026, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.68, p5-Graph-0.9704,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, 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-SSL-2.056, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.016, p5-Moo-2.003004, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.000006, p5-SVG-2.84, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.29, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.005001, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002002, p5-Type-Tiny-XS-0.014, p5-Types-Serialiser-1.0_1, p5-URI-1.74, 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-2.0132,1, 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-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.24, p5-YAML-LibYAML-0.67, p5-common-sense-3.74, p5-libwww-6.33, p5-libxml-0.08_1, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, printproto-1.0.5, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, tiff-4.0.9_1, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
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: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, graphite2-1.3.11, graphviz-2.40.1_5, harfbuzz-1.8.1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libevent-2.1.8_1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.2,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mysql56-client-5.6.40, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.1, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007002, p5-CGI-4.38, p5-Class-Method-Modifiers-2.12, p5-Clone-0.39, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.046, p5-DBI-1.641, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17026, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.68, p5-Graph-0.9704,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, 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-SSL-2.056, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.016, p5-Moo-2.003004, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.000006, p5-SVG-2.84, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.29, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.005001, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002002, p5-Type-Tiny-XS-0.014, p5-Types-Serialiser-1.0_1, p5-URI-1.74, 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-2.0132,1, 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-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.24, p5-YAML-LibYAML-0.67, p5-common-sense-3.74, p5-libwww-6.33, p5-libxml-0.08_1, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, printproto-1.0.5, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, tiff-4.0.9_1, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
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: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, graphite2-1.3.11, graphviz-2.40.1_5, harfbuzz-1.8.1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libevent-2.1.8_1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.2,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mysql56-client-5.6.40, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.1, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007002, p5-CGI-4.38, p5-Class-Method-Modifiers-2.12, p5-Clone-0.39, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.046, p5-DBI-1.641, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17026, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.68, p5-Graph-0.9704,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, 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-SSL-2.056, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.016, p5-Moo-2.003004, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.000006, p5-SVG-2.84, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.29, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.005001, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002002, p5-Type-Tiny-XS-0.014, p5-Types-Serialiser-1.0_1, p5-URI-1.74, 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-2.0132,1, 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-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.24, p5-YAML-LibYAML-0.67, p5-common-sense-3.74, p5-libwww-6.33, p5-libxml-0.08_1, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, printproto-1.0.5, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, tiff-4.0.9_1, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
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-3.37.3, curl-7.60.0, libnghttp2-1.32.0, 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-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.056, p5-LWP-MediaTypes-6.02_1, p5-Module-Build-0.4224, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-Readonly-2.05, p5-Try-Tiny-0.28, p5-URI-1.74, p5-WWW-Curl-4.17_2, p5-WWW-RobotRules-6.02_1, p5-libwww-6.33, perl5-5.26.2
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: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, graphite2-1.3.11, graphviz-2.40.1_5, harfbuzz-1.8.1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libevent-2.1.8_1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.2,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mysql56-client-5.6.40, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.1, p5-Authen-NTLM-1.09_1, p5-BioPerl-1.007002, p5-CGI-4.38, p5-Class-Method-Modifiers-2.12, p5-Clone-0.39, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.046, p5-DBI-1.641, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17026, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.68, p5-Graph-0.9704,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, 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-SSL-2.056, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Runtime-0.016, p5-Moo-2.003004, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.000006, p5-SVG-2.84, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.29, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.005001, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002002, p5-Type-Tiny-XS-0.014, p5-Types-Serialiser-1.0_1, p5-URI-1.74, 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-2.0132,1, 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-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.24, p5-YAML-LibYAML-0.67, p5-common-sense-3.74, p5-libwww-6.33, p5-libxml-0.08_1, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, printproto-1.0.5, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, tiff-4.0.9_1, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
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-1.000000, p5-File-ReadBackwards-1.05_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-URI-1.74, perl5-5.26.2
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-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, p5-HTTP-Negotiate-6.01_1, p5-IO-HTML-1.001_1, p5-IO-Socket-SSL-2.056, p5-LWP-MediaTypes-6.02_1, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-Try-Tiny-0.28, p5-URI-1.74, p5-WWW-RobotRules-6.02_1, p5-libwww-6.33, perl5-5.26.2
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-3.37.3, cairo-1.14.8_1,2, curl-7.60.0, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, graphite2-1.3.11, graphviz-2.40.1_5, harfbuzz-1.8.1, indexinfo-0.3.1, io_lib-1.14.9, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libevent-2.1.8_1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.2,1, libnghttp2-1.32.0, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mysql56-client-5.6.40, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.1, p5-Authen-NTLM-1.09_1, p5-Bio-Coordinate-1.007001, p5-Bio-SCF-1.03_1, p5-BioPerl-1.007002, p5-CGI-4.38, p5-Class-Method-Modifiers-2.12, p5-Clone-0.39, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.046, p5-DBI-1.641, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17026, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.68, p5-GD-SVG-0.33_6, p5-Graph-0.9704,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, 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-SSL-2.056, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Build-0.4224, p5-Module-Runtime-0.016, p5-Moo-2.003004, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.000006, p5-SVG-2.84, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.29, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.005001, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002002, p5-Type-Tiny-XS-0.014, p5-Types-Serialiser-1.0_1, p5-URI-1.74, 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-2.0132,1, 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-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.24, p5-YAML-LibYAML-0.67, p5-common-sense-3.74, p5-libwww-6.33, p5-libxml-0.08_1, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, printproto-1.0.5, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, tiff-4.0.9_1, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-Bio-MAGETAB-1.31_1
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-6.06, p5-Class-C3-0.34, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.32, 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-6.70, p5-DateTime-1.49, p5-DateTime-Format-DateManip-0.04_1, p5-DateTime-Locale-1.20, p5-DateTime-TimeZone-2.19,1, 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-1.200, p5-Eval-Closure-0.14, p5-Exception-Class-1.44, p5-File-ShareDir-1.110, 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-1.15,1, p5-Net-Domain-TLD-1.74, p5-Package-DeprecationManager-0.17_1, p5-Package-Stash-0.37_1, p5-Package-Stash-XS-0.28_2, p5-Params-Coerce-0.14_2, p5-Params-Util-1.07_2, p5-Params-Validate-1.29, p5-Params-ValidationCompiler-0.27, p5-Parse-RecDescent-1.967.009_2, p5-Role-Tiny-2.000006, p5-Scalar-List-Utils-1.50,1, p5-Specio-0.42, 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-2.005001, p5-Text-CSV_XS-1.34, p5-TimeDate-2.30_2,1, p5-Try-Tiny-0.28, p5-URI-1.74, p5-Variable-Magic-0.62, p5-namespace-autoclean-0.28, p5-namespace-clean-0.27, perl5-5.26.2
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, perl5-5.26.2
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: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, graphite2-1.3.11, graphviz-2.40.1_5, harfbuzz-1.8.1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libevent-2.1.8_1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.2,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mysql56-client-5.6.40, p5-Algorithm-C3-0.10_1, p5-Algorithm-Combinatorics-0.27_1, p5-Algorithm-Munkres-0.08_1, p5-Archive-Zip-1.60, p5-Array-Compare-3.0.1, p5-Authen-NTLM-1.09_1, p5-B-Hooks-EndOfScope-0.24, p5-BioPerl-1.007002, p5-CGI-4.38, p5-Cache-LRU-0.04_1, p5-Class-C3-0.34, p5-Class-Data-Inheritable-0.08_1, p5-Class-Inspector-1.32, p5-Class-Load-0.25, p5-Class-Load-XS-0.10, p5-Class-Method-Modifiers-2.12, p5-Class-Singleton-1.5_1, p5-Clone-0.39, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-SQLite-1.58, p5-DBD-mysql-4.046, p5-DBI-1.641, p5-DBIx-Connector-0.56, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Data-TemporaryBag-0.09_1, p5-Data-UUID-1.221, p5-DateTime-1.49, p5-DateTime-Format-W3CDTF-0.07, p5-DateTime-Locale-1.20, p5-DateTime-TimeZone-2.19,1, p5-Devel-GlobalDestruction-0.14, p5-Devel-OverloadInfo-0.005, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Dist-CheckConflicts-0.11_1, p5-Encode-Locale-1.05, p5-Error-0.17026, p5-Eval-Closure-0.14, p5-Exception-Class-1.44, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-ShareDir-1.110, p5-File-Slurp-Tiny-0.004, p5-Font-TTF-1.06, p5-GD-2.68, p5-Graph-0.9704,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, 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-SSL-2.056, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-2.97.001, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, 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-Derivative-1.01, p5-Math-Random-0.72, p5-Math-Spline-0.02_1, 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-Moose-2.2011,1, p5-MooseX-ArrayRef-0.005, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-OLE-Storage_Lite-0.19_1, p5-PDF-API2-2.033, p5-Package-DeprecationManager-0.17_1, p5-Package-Stash-0.37_1, p5-Package-Stash-XS-0.28_2, p5-Params-Util-1.07_2, p5-Params-Validate-1.29, p5-Params-ValidationCompiler-0.27, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-RDF-Query-2.918, p5-RDF-Trine-1.015_2, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.000006, p5-SVG-2.84, p5-SVG-Graph-0.04_1, 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-Sort-Naturally-1.03_1, p5-Specio-0.42, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, 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-2.005001, p5-Term-ANSIColor-4.06, p5-Text-Aligner-0.13, p5-Text-CSV-1.95, p5-Text-Iconv-1.7_3, p5-Text-Table-1.133, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002002, p5-Type-Tiny-XS-0.014, p5-Types-Serialiser-1.0_1, p5-URI-1.74, p5-Unicode-Escape-0.0.2_1, p5-Unicode-String-2.10, 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-2.0132,1, 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-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-XML2JSON-0.06_1, p5-XML-XPath-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.24, p5-YAML-LibYAML-0.67, p5-YAML-Syck-1.27_1, p5-common-sense-3.74, p5-libwww-6.33, p5-libxml-0.08_1, p5-namespace-autoclean-0.28, p5-namespace-clean-0.27, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, printproto-1.0.5, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, tiff-4.0.9_1, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-Bio-SCF-1.03_1
Read and Update SCF Chromatographic Sequence Files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: ca_root_nss-3.37.3, curl-7.60.0, io_lib-1.14.9, libnghttp2-1.32.0, perl5-5.26.2
Also listed in: Perl5

p5-BioPerl-1.007002
Collection of Perl modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, graphite2-1.3.11, graphviz-2.40.1_5, harfbuzz-1.8.1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libevent-2.1.8_1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.2,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mysql56-client-5.6.40, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.1, p5-Authen-NTLM-1.09_1, p5-CGI-4.38, p5-Class-Method-Modifiers-2.12, p5-Clone-0.39, p5-Convert-Binary-C-0.78, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.046, p5-DBI-1.641, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17026, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-GD-2.68, p5-Graph-0.9704,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, 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-SSL-2.056, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Build-0.4224, p5-Module-Runtime-0.016, p5-Moo-2.003004, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.000006, p5-SVG-2.84, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.29, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.005001, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002002, p5-Type-Tiny-XS-0.014, p5-Types-Serialiser-1.0_1, p5-URI-1.74, 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-2.0132,1, 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-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.24, p5-YAML-LibYAML-0.67, p5-common-sense-3.74, p5-libwww-6.33, p5-libxml-0.08_1, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, printproto-1.0.5, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, tiff-4.0.9_1, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-BioPerl-Run-1.007002
Wrapper modules for common bioinformatics tools
Long description | Changes | Main Web Site
Maintained by: perl@FreeBSD.org
Requires: cairo-1.14.8_1,2, damageproto-1.2.1, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, graphite2-1.3.11, graphviz-2.40.1_5, harfbuzz-1.8.1, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libedit-3.1.20170329_2,1, libevent-2.1.8_1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libiconv-1.14_11, libltdl-2.4.6, liblz4-1.8.2,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mysql56-client-5.6.40, p5-Algorithm-Diff-1.1903, p5-Algorithm-Munkres-0.08_1, p5-Array-Compare-3.0.1, p5-Authen-NTLM-1.09_1, p5-Bio-FeatureIO-1.6.905, p5-BioPerl-1.007002, p5-CGI-4.38, p5-Class-Method-Modifiers-2.12, p5-Clone-0.39, p5-Config-Any-0.32, p5-Config-General-2.63, p5-Config-Tiny-2.23, p5-Convert-Binary-C-0.78, p5-Cpanel-JSON-XS-4.02, p5-Crypt-RC4-2.02_1, p5-DBD-mysql-4.046, p5-DBI-1.641, p5-Data-OptList-0.110, p5-Data-Stag-0.14_2, p5-Devel-GlobalDestruction-0.14, p5-Devel-StackTrace-2.03, p5-Digest-HMAC-1.03_1, p5-Digest-Perl-MD5-1.9_1, p5-Encode-Locale-1.05, p5-Error-0.17026, p5-Exporter-Tiny-1.000000, p5-ExtUtils-PkgConfig-1.16, p5-File-Listing-6.04_1, p5-File-Slurp-Tiny-0.004, p5-File-Sort-1.01_1, p5-GD-2.68, p5-Graph-0.9704,1, p5-GraphViz-2.24, p5-HTML-Element-Extended-1.18_1, p5-HTML-Parser-3.72, p5-HTML-TableExtract-2.15, p5-HTML-Tagset-3.20_1, p5-HTML-Tree-5.07, p5-HTTP-Cookies-6.04, p5-HTTP-Daemon-6.01_1, p5-HTTP-Date-6.02_1, p5-HTTP-Message-6.17, 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-SSL-2.056, p5-IO-String-1.08_1, p5-IO-Tty-1.12_2, p5-IO-stringy-2.111, p5-IPC-Run-0.99, p5-Inline-0.80, p5-Inline-C-0.78, p5-JSON-XS-3.04, p5-LWP-MediaTypes-6.02_1, p5-List-MoreUtils-0.428, p5-List-MoreUtils-XS-0.428, p5-Math-Derivative-1.01, p5-Math-Spline-0.02_1, p5-Module-Build-0.4224, p5-Module-Pluggable-5.2, p5-Module-Runtime-0.016, p5-Moo-2.003004, p5-Mozilla-CA-20180117, p5-Net-HTTP-6.18, p5-Net-SSLeay-1.85, p5-OLE-Storage_Lite-0.19_1, p5-Params-Util-1.07_2, p5-Parse-RecDescent-1.967.009_2, p5-Pegex-0.64, p5-PostScript-0.06_2, p5-Ref-Util-XS-0.117, p5-Role-Tiny-2.000006, p5-SVG-2.84, p5-SVG-Graph-0.04_1, p5-Set-Scalar-1.29, p5-Sort-Naturally-1.03_1, p5-Spreadsheet-ParseExcel-0.65_2,1, p5-Statistics-Descriptive-3.0609_1, p5-Sub-Exporter-0.987_1, p5-Sub-Exporter-Progressive-0.001013, p5-Sub-Install-0.928_1, p5-Sub-Quote-2.005001, p5-Text-Iconv-1.7_3, p5-Tie-IxHash-1.23_1, p5-Tree-DAG_Node-1.31, p5-Try-Tiny-0.28, p5-Type-Tie-0.009_1, p5-Type-Tiny-1.002002, p5-Type-Tiny-XS-0.014, p5-Types-Serialiser-1.0_1, p5-URI-1.74, 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-2.0132,1, 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-1.42, p5-XML-XPathEngine-0.14_1, p5-YAML-1.24, p5-YAML-LibYAML-0.67, p5-common-sense-3.74, p5-libwww-6.33, p5-libxml-0.08_1, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, printproto-1.0.5, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, tiff-4.0.9_1, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
Also listed in: Perl5

p5-TrimGalore-0.4.5
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_1, dejavu-2.37, expat-2.2.5, fastqc-0.11.5, fixesproto-5.0, fontconfig-2.12.6,1, freetype2-2.9.1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, indexinfo-0.3.1, inputproto-2.3.2, java-zoneinfo-2018.e, javavmwrapper-2.6, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libffi-3.2.1_2, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, mkfontdir-1.0.7, mkfontscale-1.1.3, openjdk8-8.172.11, perl5-5.26.2, py27-xopen-0.2.1, py36-cutadapt-1.14, py36-setuptools-39.2.0, python27-2.7.15, python36-3.6.5, readline-7.0.3_1, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.31
Also listed in: Perl5

p5-transdecoder-2.1.0_1
Identify candidate coding regions within transcript sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.30_3,1, cd-hit-4.6.6_3, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, mpc-1.1.0_1, mpfr-4.0.1, p5-URI-1.74, perl5-5.26.2
Also listed in: Perl5

paml-4.9h
Phylogenetic Analysis by Maximum Likelihood (PAML)
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1

pbbam-g20180416
PacBio BAM C++ library, with SWIG bindings
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: boost-libs-1.67.0_1, ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gettext-runtime-0.19.8.1_1, htslib-1.6, icu-61.1,1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, ninja-1.8.2,2, pkgconf-1.4.2,1, python27-2.7.15, readline-7.0.3_1, rhash-1.3.5

pbcopper-g20180413
Core C++ library for Pacific Biosciences tools
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: boost-libs-1.67.0_1, ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gettext-runtime-0.19.8.1_1, icu-61.1,1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, ninja-1.8.2,2, python27-2.7.15, readline-7.0.3_1, rhash-1.3.5

pbseqan-g20171002
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-4.4.23, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXaw-1.0.13,2, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXmu-1.1.2_3,1, libXp-1.0.3,1, libXpm-3.5.12, libXt-1.1.5,1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, printproto-1.0.5, xextproto-7.3.0, xproto-7.0.31

phyml-3.3.20180214
Simple, fast, and accurate algorithm to estimate large phylogenies
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.16.1, indexinfo-0.3.1, libtool-2.4.6, m4-1.4.18,1, perl5-5.26.2, pkgconf-1.4.2,1

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_1, gmake-4.2.1_2, 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_1, gmake-4.2.1_2, indexinfo-0.3.1

protomol-2.0.3_13
OO, component based, framework for molecular dynamics (MD) simulations
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: damageproto-1.2.1, expat-2.2.5, fixesproto-5.0, freeglut-3.0.0_1, inputproto-2.3.2, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libGLU-9.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXmu-1.1.2_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, pciids-20180428, png-1.6.34, randrproto-1.5.0, renderproto-0.11.1, tiff-4.0.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xproto-7.0.31

psi88-1.0_12
Plotting wavefunctions (molecular orbitals) in 3D
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.30_3,1, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, mpc-1.1.0_1, mpfr-4.0.1

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_1, indexinfo-0.3.1, libffi-3.2.1_2, py27-certifi-2018.4.16, py27-chardet-3.0.4, py27-idna-2.6, py27-openssl-17.5.0_1, py27-slumber-0.7.1, py36-asn1crypto-0.22.0, py36-cffi-1.11.5, py36-cryptography-2.1.4, py36-pycparser-2.18, py36-pysocks-1.6.8, py36-requests-2.18.4, py36-setuptools-39.2.0, py36-six-1.11.0, py36-urllib3-1.22,1, python27-2.7.15, python36-3.6.5, readline-7.0.3_1
Also listed in: Python

py27-biom-format-2.1.6_2
Biological Observation Matrix (BIOM) Format Project
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.30_3,1, blas-3.5.0_4, cblas-1.0_8, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, hdf-szip-2.1_2, hdf5-1.10.1_1, indexinfo-0.3.1, lapack-3.5.0_4, libffi-3.2.1_2, metis-5.1.0_4, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, perl5-5.26.2, postgresql95-client-9.5.13, py27-bottleneck-1.2.1_3, py27-click-6.7, py27-pandas-0.23.0, py27-pyqi-0.3.2, py27-pytz-2018.4,1, py27-scipy-1.1.0, py34-numpy-1.14.3,1, py36-dateutil-2.6.1, py36-future-0.16.0, py36-h5py-2.8.0, py36-numexpr-2.6.5, py36-setuptools-39.2.0, py36-six-1.11.0, py36-sqlite3-3.6.5_7, python27-2.7.15, python34-3.4.8, python36-3.6.5, readline-7.0.3_1, sqlite3-3.24.0, suitesparse-5.2.0
Also listed in: Python

py27-biopython-1.71_1
Collection of Python modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: adobe-cmaps-20051217_3, binutils-2.30_3,1, blas-3.5.0_4, cblas-1.0_8, expat-2.2.5, fontconfig-2.12.6,1, freetype2-2.9.1, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, gmp-6.1.2, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, lapack-3.5.0_4, lcms2-2.9, libX11-1.6.5,1, libXScrnSaver-1.2.2_3, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXft-2.3.2_1, libXrender-0.9.10, libffi-3.2.1_2, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, metis-5.1.0_4, mkfontdir-1.0.7, mkfontscale-1.1.3, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, openjpeg-2.3.0, png-1.6.34, py27-pillow-5.0.0, py34-numpy-1.14.3,1, py35-tkinter-3.5.5_6, py36-reportlab-3.2.0, py36-setuptools-39.2.0, python27-2.7.15, python34-3.4.8, python35-3.5.5, python36-3.6.5, readline-7.0.3_1, renderproto-0.11.1, scrnsaverproto-1.2.2, suitesparse-5.2.0, tcl86-8.6.8, tiff-4.0.9_1, tk86-8.6.8_2, webp-1.0.0, xextproto-7.3.0, xproto-7.0.31
Also listed in: Python

py27-bx-python-0.8.1_1
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.30_3,1, blas-3.5.0_4, cblas-1.0_8, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, lapack-3.5.0_4, libffi-3.2.1_2, lzo2-2.10_1, metis-5.1.0_4, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, py34-cython-0.28.2, py34-numpy-1.14.3,1, py36-python-lzo-1.12, py36-setuptools-39.2.0, python27-2.7.15, python34-3.4.8, python36-3.6.5, readline-7.0.3_1, suitesparse-5.2.0
Also listed in: Python

py27-cutadapt-1.14
Finds and removes adapter sequences, primers, poly-A tails, etc
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, libffi-3.2.1_2, py27-xopen-0.2.1, py36-setuptools-39.2.0, python27-2.7.15, python36-3.6.5, readline-7.0.3_1
Also listed in: Python

py27-macs2-2.1.0.p20170505_1
Analysis of chromatin immunoprecipitation (ChIP) sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: binutils-2.30_3,1, blas-3.5.0_4, cblas-1.0_8, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, lapack-3.5.0_4, libffi-3.2.1_2, metis-5.1.0_4, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, py34-cython-0.28.2, py34-numpy-1.14.3,1, py36-setuptools-39.2.0, python27-2.7.15, python34-3.4.8, python36-3.6.5, readline-7.0.3_1, suitesparse-5.2.0
Also listed in: Python

py27-pyfasta-0.5.2_2
Fast, memory-efficient, pythonic access to fasta sequence files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: binutils-2.30_3,1, blas-3.5.0_4, cblas-1.0_8, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, lapack-3.5.0_4, libffi-3.2.1_2, metis-5.1.0_4, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, py34-numpy-1.14.3,1, py36-setuptools-39.2.0, python27-2.7.15, python34-3.4.8, python36-3.6.5, readline-7.0.3_1, suitesparse-5.2.0
Also listed in: Python

py27-pymol-2.1.0_2
OpenGL-based molecular visualization system
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: avahi-app-0.6.31_6, binutils-2.30_3,1, blas-3.5.0_4, blt-2.5.3_3, ca_root_nss-3.37.3, cairo-1.14.8_1,2, cblas-1.0_8, cups-2.2.8_1, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dri2proto-2.8, dri3proto-1.0, expat-2.2.5, fixesproto-5.0, fontcacheproto-0.1.3, fontconfig-2.12.6,1, freeglut-3.0.0_1, freetype2-2.9.1, gcc-ecj-4.5, gcc6-6.4.0_7, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glew-2.1.0, glib-2.50.3_3,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, harfbuzz-1.8.1, hicolor-icon-theme-0.15, icu-61.1,1, indexinfo-0.3.1, inputproto-2.3.2, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, lapack-3.5.0_4, lcms-1.19_6,1, libGLU-9.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXScrnSaver-1.2.2_3, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXfontcache-1.0.5_3, libXft-2.3.2_1, libXi-1.7.9,1, libXmu-1.1.2_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.92,1, libffi-3.2.1_2, libiconv-1.14_11, libidn2-2.0.5, libmng-1.0.10_3, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libxcb-1.13, libxkbcommon-0.8.0, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, metis-5.1.0_4, mpc-1.1.0_1, mpfr-4.0.1, msgpack-3.0.1, nettle-3.4, openblas-0.2.20_2,1, p11-kit-0.23.12, pciids-20180428, pcre-8.42, pcre2-10.21_1, perl5-5.26.2, pixman-0.34.0, png-1.6.34, py27-msgpack-0.5.6, py27-qt5-opengl-5.9.2_5, py34-numpy-1.14.3,1, py35-tkinter-3.5.5_6, py36-Pmw-2.0.1, py36-qt5-core-5.9.2_6, py36-qt5-gui-5.9.2_2, py36-qt5-widgets-5.9.2_5, py36-setuptools-39.2.0, python27-2.7.15, python34-3.4.8, python35-3.5.5, python36-3.6.5, qscintilla2-qt5-2.10.4, qt5-core-5.10.1_2, qt5-dbus-5.10.1, qt5-gui-5.10.1, qt5-imageformats-5.10.1, qt5-network-5.10.1, qt5-opengl-5.10.1, qt5-printsupport-5.10.1, qt5-widgets-5.10.1, qtchooser-39, randrproto-1.5.0, readline-7.0.3_1, renderproto-0.11.1, scrnsaverproto-1.2.2, suitesparse-5.2.0, tcl86-8.6.8, tiff-4.0.9_1, tk86-8.6.8_2, tpm-emulator-0.7.4_2, trousers-0.3.14_2, webp-1.0.0, 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-1.1.1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xprop-1.2.3, xproto-7.0.31, xset-1.2.4
Also listed in: Science, Python

py27-pysam-0.14.1
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_1, gmake-4.2.1_2, indexinfo-0.3.1, libffi-3.2.1_2, py34-cython-0.28.2, py36-setuptools-39.2.0, python27-2.7.15, python34-3.4.8, python36-3.6.5, readline-7.0.3_1
Also listed in: Python

py27-python-nexus-1.61
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_1, indexinfo-0.3.1, libffi-3.2.1_2, py36-setuptools-39.2.0, python27-2.7.15, python36-3.6.5, readline-7.0.3_1
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_1, indexinfo-0.3.1, libffi-3.2.1_2, py27-certifi-2018.4.16, py27-chardet-3.0.4, py27-idna-2.6, py27-openssl-17.5.0_1, py27-slumber-0.7.1, py36-asn1crypto-0.22.0, py36-cffi-1.11.5, py36-cryptography-2.1.4, py36-pycparser-2.18, py36-pysocks-1.6.8, py36-requests-2.18.4, py36-setuptools-39.2.0, py36-six-1.11.0, py36-urllib3-1.22,1, python27-2.7.15, python36-3.6.5, readline-7.0.3_1
Also listed in: Python

py36-biom-format-2.1.6_2
Biological Observation Matrix (BIOM) Format Project
Long description | Changes | Main Web Site
Maintained by: jrm@FreeBSD.org
Requires: binutils-2.30_3,1, blas-3.5.0_4, cblas-1.0_8, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, hdf-szip-2.1_2, hdf5-1.10.1_1, indexinfo-0.3.1, lapack-3.5.0_4, libffi-3.2.1_2, metis-5.1.0_4, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, py27-bottleneck-1.2.1_3, py27-click-6.7, py27-pandas-0.23.0, py27-pytz-2018.4,1, py27-scipy-1.1.0, py34-numpy-1.14.3,1, py36-dateutil-2.6.1, py36-future-0.16.0, py36-h5py-2.8.0, py36-numexpr-2.6.5, py36-setuptools-39.2.0, py36-six-1.11.0, py36-sqlite3-3.6.5_7, python27-2.7.15, python34-3.4.8, python36-3.6.5, readline-7.0.3_1, sqlite3-3.24.0, suitesparse-5.2.0
Also listed in: Python

py36-biopython-1.71_1
Collection of Python modules for bioinformatics
Long description | Changes | Main Web Site
Maintained by: mauricio@arareko.net
Requires: adobe-cmaps-20051217_3, binutils-2.30_3,1, blas-3.5.0_4, cblas-1.0_8, expat-2.2.5, fontconfig-2.12.6,1, freetype2-2.9.1, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, giflib-5.1.4, gmp-6.1.2, indexinfo-0.3.1, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, lapack-3.5.0_4, lcms2-2.9, libX11-1.6.5,1, libXScrnSaver-1.2.2_3, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXft-2.3.2_1, libXrender-0.9.10, libffi-3.2.1_2, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, metis-5.1.0_4, mkfontdir-1.0.7, mkfontscale-1.1.3, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, openjpeg-2.3.0, png-1.6.34, py27-pillow-5.0.0, py34-numpy-1.14.3,1, py35-tkinter-3.5.5_6, py36-reportlab-3.2.0, py36-setuptools-39.2.0, python27-2.7.15, python34-3.4.8, python35-3.5.5, python36-3.6.5, readline-7.0.3_1, renderproto-0.11.1, scrnsaverproto-1.2.2, suitesparse-5.2.0, tcl86-8.6.8, tiff-4.0.9_1, tk86-8.6.8_2, webp-1.0.0, xextproto-7.3.0, xproto-7.0.31
Also listed in: Python

py36-bx-python-0.8.1_1
Python module for reading, manipulating and writing genomic data sets
Long description | Changes | Main Web Site
Maintained by: yuri@FreeBSD.org
Requires: binutils-2.30_3,1, blas-3.5.0_4, cblas-1.0_8, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, lapack-3.5.0_4, libffi-3.2.1_2, lzo2-2.10_1, metis-5.1.0_4, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, py34-cython-0.28.2, py34-numpy-1.14.3,1, py36-python-lzo-1.12, py36-setuptools-39.2.0, python34-3.4.8, python36-3.6.5, readline-7.0.3_1, suitesparse-5.2.0
Also listed in: Python

py36-cutadapt-1.14
Finds and removes adapter sequences, primers, poly-A tails, etc
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, indexinfo-0.3.1, libffi-3.2.1_2, py27-xopen-0.2.1, py36-setuptools-39.2.0, python27-2.7.15, python36-3.6.5, readline-7.0.3_1
Also listed in: Python

py36-orange3-bioinformatics-3.1.0
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_1, avahi-app-0.6.31_6, binutils-2.30_3,1, blas-3.5.0_4, ca_root_nss-3.37.3, cairo-1.14.8_1,2, cblas-1.0_8, compositeproto-0.4.2, cups-2.2.8_1, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, ffmpeg-4.0_1,1, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontcacheproto-0.1.3, fontconfig-2.12.6,1, freeglut-3.0.0_1, freetype2-2.9.1, fribidi-0.19.7, gcc-ecj-4.5, gcc6-6.4.0_7, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, harfbuzz-1.8.1, hicolor-icon-theme-0.15, icu-61.1,1, indexinfo-0.3.1, inputproto-2.3.2, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.3, jsoncpp-1.8.1_3, kbproto-1.0.7, lapack-3.5.0_4, lcms-1.19_6,1, lcms2-2.9, leptonica-1.76.0, libGLU-9.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXScrnSaver-1.2.2_3, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.15, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXfontcache-1.0.5_3, libXft-2.3.2_1, libXi-1.7.9,1, libXmu-1.1.2_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.92,1, libevent-2.1.8_1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgcrypt-1.8.3, libgpg-error-1.31, libiconv-1.14_11, libidn2-2.0.5, libmng-1.0.10_3, libogg-1.3.3,4, libpaper-1.1.24.4, libpci-3.5.6_1, libpciaccess-0.13.5, libpthread-stubs-0.4, libsrtp-1.6.0_1, libtasn1-4.13, libtheora-1.1.1_7, libunistring-0.9.10, libunwind-20170615, libv4l-1.6.3_2, libva-2.1.0, libvdpau-1.1.1, libvorbis-1.3.6,3, libvpx-1.7.0, libx264-0.152.2854, libxcb-1.13, libxkbcommon-0.8.0, libxml2-2.9.7, libxshmfence-1.2_2, libxslt-1.1.32, mesa-libs-18.1.2, metis-5.1.0_4, mkfontdir-1.0.7, mkfontscale-1.1.3, mpc-1.1.0_1, mpfr-4.0.1, nettle-3.4, nspr-4.19, nss-3.37.3, openblas-0.2.20_2,1, opencv-core-3.4.1_1, openjpeg-2.3.0, opus-1.2.1, orange3-3.13.0.120, p11-kit-0.23.12, pango-1.42.0, pciids-20180428, pcre-8.42, pcre2-10.21_1, perl5-5.26.2, pixman-0.34.0, png-1.6.34, protobuf-3.5.2, py27-Genesis-PyAPI-1.2.1, py27-PyOpenGL-3.1.0_2, py27-bottleneck-1.2.1_3, py27-certifi-2018.4.16, py27-chardet-3.0.4, py27-dbus-1.2.0_1, py27-idna-2.6, py27-joblib-0.9.4, py27-keyring-12.0.1, py27-keyrings.alt-3.0, py27-openssl-17.5.0_1, py27-pillow-5.0.0, py27-qt5-qml-5.9.2_5, py27-qt5-webchannel-5.9.2_4, py27-qt5-webengine-5.9.2_4, py27-scipy-1.1.0, py27-serverfiles-0.2.1, py27-slumber-0.7.1, py27-xlrd-1.0.0, py34-numpy-1.14.3,1, py35-tkinter-3.5.5_6, py36-AnyQt-0.0.8, py36-CommonMark-0.7.5_1, py36-SecretStorage-2.3.1, py36-asn1crypto-0.22.0, py36-cffi-1.11.5, py36-cryptography-2.1.4, py36-docutils-0.14_3, py36-entrypoints-0.2.3, py36-future-0.16.0, py36-pycparser-2.18, py36-pyqtgraph-0.10.0, py36-pysocks-1.6.8, py36-qt5-core-5.9.2_6, py36-qt5-gui-5.9.2_2, py36-qt5-network-5.9.2_5, py36-qt5-printsupport-5.9.2_5, py36-qt5-widgets-5.9.2_5, py36-requests-2.18.4, py36-requests-cache-0.4.13, py36-scikit-learn-0.19.1_1, py36-setuptools-39.2.0, py36-six-1.11.0, py36-urllib3-1.22,1, pydbus-common-1.2.0_2, python27-2.7.15, python34-3.4.8, python35-3.5.5, python36-3.6.5, qscintilla2-qt5-2.10.4, qt5-assistant-5.10.1, qt5-concurrent-5.10.1, qt5-core-5.10.1_2, qt5-dbus-5.10.1, qt5-designer-5.10.1, qt5-gui-5.10.1, qt5-help-5.10.1, qt5-imageformats-5.10.1, qt5-location-5.10.1, qt5-network-5.10.1, qt5-printsupport-5.10.1, qt5-qml-5.10.1, qt5-quick-5.10.1, qt5-sql-5.10.1, qt5-sqldrivers-sqlite3-5.10.1, qt5-testlib-5.10.1, qt5-uiplugin-5.10.1, qt5-webchannel-5.10.1, qt5-webengine-5.9.5_1, qt5-widgets-5.10.1, qt5-xml-5.10.1, qt5-xmlpatterns-5.10.1, qtchooser-39, randrproto-1.5.0, re2-20180401, readline-7.0.3_1, recordproto-1.14.2, renderproto-0.11.1, scrnsaverproto-1.2.2, snappy-1.1.6, sqlite3-3.24.0, suitesparse-5.2.0, tcl86-8.6.8, tesseract-3.05.01_4, tesseract-data-3.04.00, tiff-4.0.9_1, tk86-8.6.8_2, tpm-emulator-0.7.4_2, trousers-0.3.14_2, v4l_compat-1.6.3, webp-1.0.0, x265-2.6_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-1.1.1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xprop-1.2.3, xproto-7.0.31, xset-1.2.4, xvid-1.3.4,1
Also listed in: Python

py36-pyfasta-0.5.2_2
Fast, memory-efficient, pythonic access to fasta sequence files
Long description | Changes | Main Web Site
Maintained by: wen@FreeBSD.org
Requires: binutils-2.30_3,1, blas-3.5.0_4, cblas-1.0_8, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, lapack-3.5.0_4, libffi-3.2.1_2, metis-5.1.0_4, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, py34-numpy-1.14.3,1, py36-setuptools-39.2.0, python34-3.4.8, python36-3.6.5, readline-7.0.3_1, suitesparse-5.2.0
Also listed in: Python

py36-pysam-0.14.1
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_1, gmake-4.2.1_2, indexinfo-0.3.1, libffi-3.2.1_2, py34-cython-0.28.2, py36-setuptools-39.2.0, python34-3.4.8, python36-3.6.5, readline-7.0.3_1
Also listed in: Python

py36-python-nexus-1.61
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_1, indexinfo-0.3.1, libffi-3.2.1_2, py36-setuptools-39.2.0, python36-3.6.5, readline-7.0.3_1
Also listed in: Python

pycogent-1.9_1
Toolkit for statistical analysis of biological sequences
Long description | Changes | Main Web Site
Maintained by: python@FreeBSD.org
Requires: binutils-2.30_3,1, blas-3.5.0_4, ca_root_nss-3.37.3, cblas-1.0_8, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, lapack-3.5.0_4, libffi-3.2.1_2, metis-5.1.0_4, mpc-1.1.0_1, mpfr-4.0.1, openblas-0.2.20_2,1, py27-Babel-2.5.3, py27-Jinja2-2.10, py27-certifi-2018.4.16, py27-chardet-3.0.4, py27-idna-2.6, py27-imagesize-0.7.1, py27-openssl-17.5.0_1, py27-pytz-2018.4,1, py27-sphinx_rtd_theme-0.2.4, py27-sphinxcontrib-websupport-1.0.1, py34-cython-0.28.2, py34-numpy-1.14.3,1, py36-MarkupSafe-1.0, py36-alabaster-0.7.6, py36-asn1crypto-0.22.0, py36-cffi-1.11.5, py36-cryptography-2.1.4, py36-docutils-0.14_3, py36-pycparser-2.18, py36-pygments-2.2.0, py36-pysocks-1.6.8, py36-pystemmer-1.3.0_1, py36-requests-2.18.4, py36-setuptools-39.2.0, py36-six-1.11.0, py36-snowballstemmer-1.2.0_1, py36-sphinx-1.6.5_1,1, py36-sqlalchemy10-1.0.14, py36-sqlite3-3.6.5_7, py36-urllib3-1.22,1, python27-2.7.15, python34-3.4.8, python36-3.6.5, readline-7.0.3_1, sqlite3-3.24.0, suitesparse-5.2.0
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_1, gmake-4.2.1_2, indexinfo-0.3.1

raster3d-3.0.2_11
Set of tools for generating raster images of proteins and molecules
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: ImageMagick-6.9.9.28,1, avahi-app-0.6.31_6, binutils-2.30_3,1, ca_root_nss-3.37.3, cairo-1.14.8_1,2, cups-2.2.8_1, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fftw3-3.3.7, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gcc-ecj-4.5, gcc6-6.4.0_7, gdbm-1.13_1, gdk-pixbuf2-2.36.11, gettext-runtime-0.19.8.1_1, ghostscript9-agpl-base-9.23, ghostscript9-agpl-x11-9.23, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, harfbuzz-1.8.1, indexinfo-0.3.1, inputproto-2.3.2, jasper-1.900.1_17, jbig2dec-0.14, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, lcms2-2.9, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libcroco-0.6.12, libdaemon-0.14_1, libdrm-2.4.92,1, libffi-3.2.1_2, libfontenc-1.1.3_1, libgd-2.2.4_1,1, libgsf-1.14.41, libiconv-1.14_11, libidn-1.34, libidn2-2.0.5, libijs-0.35_5, liblqr-1-0.4.2, libltdl-2.4.6, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libraw-0.18.8, librsvg2-2.40.20, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libwmf-0.2.8.4_15, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mpc-1.1.0_1, mpfr-4.0.1, nettle-3.4, openjpeg-2.3.0, p11-kit-0.23.12, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, poppler-data-0.4.9, python27-2.7.15, readline-7.0.3_1, renderproto-0.11.1, shared-mime-info-1.8, tiff-4.0.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, webp-1.0.0, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31
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

ruby24-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-3.1.20170329_2,1, libffi-3.2.1_2, libunwind-20170615, libyaml-0.1.6_2, ruby-2.4.4,1
Also listed in: Ruby

rubygem-bio-1.5.1
Integrated environment for Bioinformatics written in Ruby
Long description | Changes | Main Web Site
Maintained by: ruby@FreeBSD.org
Requires: indexinfo-0.3.1, libedit-3.1.20170329_2,1, libffi-3.2.1_2, libunwind-20170615, libyaml-0.1.6_2, ruby-2.4.4,1, ruby24-gems-2.7.6
Also listed in: Rubygems

samtools-1.6
Tools for manipulating next-generation sequencing data
Long description | Changes | Main Web Site
Maintained by: cartwright@asu.edu
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.16.1, ca_root_nss-3.37.3, curl-7.60.0, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, htslib-1.6, indexinfo-0.3.1, libnghttp2-1.32.0, m4-1.4.18,1, perl5-5.26.2

seaview-4.6.5
Multiple DNA/protein sequence alignment editor
Long description | Changes | Main Web Site
Maintained by: bofh@FreeBSD.org
Requires: damageproto-1.2.1, expat-2.2.5, fixesproto-5.0, fltk-1.3.4, fontconfig-2.12.6,1, freetype2-2.9.1, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, jpeg-turbo-1.5.3, kbproto-1.0.7, libGLU-9.0.0_3, libX11-1.6.5,1, libXau-1.0.8_3, libXcursor-1.1.15, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXinerama-1.1.3_3,1, libXrender-0.9.10, libXxf86vm-1.1.4_1, libdrm-2.4.92,1, libpciaccess-0.13.5, libpthread-stubs-0.4, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, pciids-20180428, png-1.6.34, renderproto-0.11.1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xproto-7.0.31

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_1
Official bioinformatic applications based on the SeqAn library
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: binutils-2.30_3,1, boost-libs-1.67.0_1, ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, icu-61.1,1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, mpc-1.1.0_1, mpfr-4.0.1, ninja-1.8.2,2, python27-2.7.15, readline-7.0.3_1, 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_2
Tools for visualising sequence alignments
Long description | Changes | Main Web Site
Maintained by: pi@FreeBSD.org
Requires: atk-2.24.0, avahi-app-0.6.31_6, ca_root_nss-3.37.3, cairo-1.14.8_1,2, compositeproto-0.4.2, cups-2.2.8_1, curl-7.60.0, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, dri2proto-2.8, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gdbm-1.13_1, gdk-pixbuf2-2.36.11, gettext-runtime-0.19.8.1_1, gettext-tools-0.19.8.1, glib-2.50.3_3,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, gtk-update-icon-cache-2.24.32, gtk2-2.24.32, harfbuzz-1.8.1, hicolor-icon-theme-0.15, indexinfo-0.3.1, inputproto-2.3.2, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXcursor-1.1.15, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXft-2.3.2_1, libXi-1.7.9,1, libXinerama-1.1.3_3,1, libXrandr-1.5.1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, libdaemon-0.14_1, libdrm-2.4.92,1, libffi-3.2.1_2, libfontenc-1.1.3_1, libiconv-1.14_11, libidn2-2.0.5, libnghttp2-1.32.0, libpaper-1.1.24.4, libpciaccess-0.13.5, libpthread-stubs-0.4, libtasn1-4.13, libunistring-0.9.10, libunwind-20170615, libxcb-1.13, libxml2-2.9.7, libxshmfence-1.2_2, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, nettle-3.4, p11-kit-0.23.12, pango-1.42.0, pciids-20180428, pcre-8.42, perl5-5.26.2, pixman-0.34.0, pkgconf-1.4.2,1, png-1.6.34, python27-2.7.15, randrproto-1.5.0, readline-7.0.3_1, renderproto-0.11.1, shared-mime-info-1.8, sqlite3-3.24.0, tiff-4.0.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, xcb-util-0.4.0_2,1, xcb-util-renderutil-0.3.9_1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xineramaproto-1.2.1, xorg-fonts-truetype-7.7_1, xproto-7.0.31

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

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_1, gmake-4.2.1_2, indexinfo-0.3.1

stacks-1.48
Software pipeline for building loci from short-read sequences
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, libffi-3.2.1_2, python27-2.7.15, readline-7.0.3_1

tRNAscan-SE-2.0.0
Searching for tRNA genes in genomic sequence
Long description | Changes | Main Web Site
Maintained by: mzaki@niid.go.jp
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.16.1, indexinfo-0.3.1, infernal-1.1.2, m4-1.4.18,1, perl5-5.26.2

t_coffee-9.03_7
Multiple DNA or protein sequence alignment package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.30_3,1, clustalw-2.1_2, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, mpc-1.1.0_1, mpfr-4.0.1

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-3.37.3, curl-7.60.0, htslib-1.6, libnghttp2-1.32.0

tinker-7.1.3_4
General purpose molecular modelling package
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: binutils-2.30_3,1, gcc-ecj-4.5, gcc6-6.4.0_7, gettext-runtime-0.19.8.1_1, gmp-6.1.2, indexinfo-0.3.1, mpc-1.1.0_1, mpfr-4.0.1

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_1, dejavu-2.37, expat-2.2.5, fixesproto-5.0, fontconfig-2.12.6,1, freetype2-2.9.1, giflib-5.1.4, inputproto-2.3.2, java-zoneinfo-2018.e, javavmwrapper-2.6, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libXrender-0.9.10, libXt-1.1.5,1, libXtst-1.2.3, libfontenc-1.1.3_1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, mkfontdir-1.0.7, mkfontscale-1.1.3, openjdk8-8.172.11, recordproto-1.14.2, renderproto-0.11.1, xextproto-7.3.0, xproto-7.0.31
Also listed in: Java

ugene-1.22.0_3
Free, open-source, cross-platform bioinformatics toolkit
Long description | Changes | Main Web Site
Maintained by: h2+fbsdports@fsfe.org
Requires: avahi-app-0.6.31_6, bash-4.4.23, ca_root_nss-3.37.3, cairo-1.14.8_1,2, compositeproto-0.4.2, cups-2.2.8_1, damageproto-1.2.1, dbus-1.10.16_1, dbus-glib-0.108, dejavu-2.37, desktop-file-utils-0.23, dri2proto-2.8, dri3proto-1.0, encodings-1.0.4_4,1, expat-2.2.5, fixesproto-5.0, font-bh-ttf-1.0.3_3, font-misc-ethiopic-1.0.3_3, font-misc-meltho-1.0.3_3, font-util-1.3.1, fontcacheproto-0.1.3, fontconfig-2.12.6,1, freetype2-2.9.1, fribidi-0.19.7, gdbm-1.13_1, gettext-runtime-0.19.8.1_1, giflib-5.1.4, glib-2.50.3_3,1, glproto-1.4.17, gmp-6.1.2, gnome_subr-1.0, gnutls-3.5.18, gobject-introspection-1.50.0_1,1, graphite2-1.3.11, gstreamer1-1.12.3, gstreamer1-libav-1.12.3_2, gstreamer1-plugins-1.12.3, gstreamer1-plugins-a52dec-1.12.3, gstreamer1-plugins-bad-1.12.3_2, gstreamer1-plugins-core-1.12, gstreamer1-plugins-dts-1.12.3, gstreamer1-plugins-dvdread-1.12.3, gstreamer1-plugins-good-1.12.3, gstreamer1-plugins-mpg123-1.12.3, gstreamer1-plugins-ogg-1.12.3, gstreamer1-plugins-pango-1.12.3, gstreamer1-plugins-png-1.12.3, gstreamer1-plugins-resindvd-1.12.3, gstreamer1-plugins-theora-1.12.3, gstreamer1-plugins-ugly-1.12.3, gstreamer1-plugins-vorbis-1.12.3, harfbuzz-1.8.1, hicolor-icon-theme-0.15, hyphen-2.8.8, icu-61.1,1, indexinfo-0.3.1, inputproto-2.3.2, iso-codes-3.76, jasper-1.900.1_17, jbigkit-2.1_1, jpeg-turbo-1.5.3, kbproto-1.0.7, lcms-1.19_6,1, libGLU-9.0.0_3, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXcomposite-0.4.4_3,1, libXdamage-1.1.4_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXfontcache-1.0.5_3, libXft-2.3.2_1, libXi-1.7.9,1, libXmu-1.1.2_3,1, libXrender-0.9.10, libXt-1.1.5,1, libXxf86vm-1.1.4_1, liba52-0.7.4_3, libdaemon-0.14_1, libdca-0.0.6, libdrm-2.4.92,1, libdvdcss-1.4.1, libdvdnav-6.0.0, libdvdread-6.0.0, libffi-3.2.1_2, libfontenc-1.1.3_1, libgcrypt-1.8.3, libgpg-error-1.31, libiconv-1.14_11, libidn2-2.0.5, 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, libtheora-1.1.1_7, libunistring-0.9.10, libunwind-20170615, libvorbis-1.3.6,3, libxcb-1.13, libxkbcommon-0.8.0, libxml2-2.9.7, libxshmfence-1.2_2, libxslt-1.1.32, mesa-libs-18.1.2, mkfontdir-1.0.7, mkfontscale-1.1.3, mpg123-1.25.10, nettle-3.4, orc-0.4.25, p11-kit-0.23.12, pango-1.42.0, pciids-20180428, pcre-8.42, pcre2-10.21_1, perl5-5.26.2, pixman-0.34.0, png-1.6.34, python27-2.7.15, qt5-buildtools-5.10.1, qt5-concurrent-5.10.1, qt5-core-5.10.1_2, qt5-dbus-5.10.1, qt5-gui-5.10.1, qt5-imageformats-5.10.1, qt5-linguisttools-5.10.1, qt5-location-5.10.1, qt5-network-5.10.1, qt5-opengl-5.10.1, qt5-printsupport-5.10.1, qt5-qmake-5.10.1, qt5-qml-5.10.1, qt5-quick-5.10.1, qt5-script-5.10.1, qt5-scripttools-5.10.1, qt5-sensors-5.10.1, qt5-sql-5.10.1, qt5-svg-5.10.1, qt5-testlib-5.10.1, qt5-webchannel-5.10.1, qt5-webkit-5.212.0.a2_9, qt5-widgets-5.10.1, qt5-xml-5.10.1, qt5-xmlpatterns-5.10.1, qtchooser-39, readline-7.0.3_1, renderproto-0.11.1, sqlite3-3.24.0, tiff-4.0.9_1, tpm-emulator-0.7.4_2, trousers-0.3.14_2, webp-1.0.0, 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-1.1.1, xextproto-7.3.0, xf86vidmodeproto-2.3.1, xorg-fonts-truetype-7.7_1, xprop-1.2.3, xproto-7.0.31, xset-1.2.4
Also listed in: Science

unanimity-g20180307
Pacific Biosciences consensus library and applications
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: boost-libs-1.67.0_1, ca_root_nss-3.37.3, cmake-3.11.3, curl-7.60.0, expat-2.2.5, gettext-runtime-0.19.8.1_1, htslib-1.6, icu-61.1,1, indexinfo-0.3.1, jsoncpp-1.8.1_3, libarchive-3.3.2,1, libffi-3.2.1_2, liblz4-1.8.2,1, libnghttp2-1.32.0, libuv-1.20.3, lzo2-2.10_1, ninja-1.8.2,2, pbbam-g20180416, pbcopper-g20180413, pbseqan-g20171002, pkgconf-1.4.2,1, python27-2.7.15, readline-7.0.3_1, rhash-1.3.5

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-3.37.3, curl-7.60.0, fastahack-g20160702, filevercmp-g20151117, fsom-g20151117, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, htslib-1.6, indexinfo-0.3.1, intervaltree-g20151213, libffi-3.2.1_2, libnghttp2-1.32.0, multichoose-1.0.3.2, python27-2.7.15, readline-7.0.3_1, smithwaterman-g20160702, tabixpp-1.0.0.10

vcftools-0.1.15
Tools for working with VCF genomics files
Long description | Changes | Main Web Site
Maintained by: jwb@FreeBSD.org
Requires: autoconf-2.69_1, autoconf-wrapper-20131203, automake-1.16.1, gettext-runtime-0.19.8.1_1, gmake-4.2.1_2, indexinfo-0.3.1, m4-1.4.18,1, perl5-5.26.2, pkgconf-1.4.2,1

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_1, gmake-4.2.1_2, indexinfo-0.3.1, libffi-3.2.1_2, perl5-5.26.2, python27-2.7.15, readline-7.0.3_1

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_1, glib-2.50.3_3,1, indexinfo-0.3.1, libffi-3.2.1_2, libiconv-1.14_11, pcre-8.42, perl5-5.26.2, pkgconf-1.4.2,1, python27-2.7.15, readline-7.0.3_1

xmolwt-0.7_7
Calculate atom weight and percent of each element for a given formula
Long description | Changes | Main Web Site
Maintained by: ports@FreeBSD.org
Requires: fixesproto-5.0, gettext-runtime-0.19.8.1_1, glib12-1.2.10_15, gmake-4.2.1_2, gtk12-1.2.10_25, indexinfo-0.3.1, inputproto-2.3.2, kbproto-1.0.7, libICE-1.0.9_1,1, libSM-1.2.2_3,1, libX11-1.6.5,1, libXau-1.0.8_3, libXdmcp-1.1.2, libXext-1.3.3_1,1, libXfixes-5.0.3, libXi-1.7.9,1, libpthread-stubs-0.4, libxcb-1.13, libxml2-2.9.7, xextproto-7.3.0, xproto-7.0.31

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