IBM Power8 Server

Model: POWER S822LC

Operating System: Centos 7

Operating System Version: 3.10.0-327.4.4.el7.ppc64le

Compiled by Shane Barrantes and The Center for Genome Research and Biocomputing

Packages

Date: June 22, 2016

Version: 1.9.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux; make; make install

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: http://www.bcgsc.ca/platform/bioinfo/software/abyss/releases/1.9.0

Date: June 23, 2016

Version: 52488

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux; make; make install

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/

Date: Feb 27, 2017

Version: 1.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: these are just perl modules

Options:

Source Download: http://www.openbioinformatics.org/annovar/annovar_download_form.php

Date: August 15, 2016

Version: 2.5.5

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: cd src; make

Options:

Source Download: http://augustus.gobics.de/binaries/

Date: Jun 22, 2016

Version: 21

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download:

Date: August 15, 2016

Version: 2016-06-15

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ./install.sh

Options:

Source Download: https://bitbucket.org/mhowison/bib/overview

Date:

Version:

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Date: Aug 26, 2016

Version: 1.3.6

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: mkdir build; cd build; cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local; make; make install

Options:

Source Download: https://github.com/genome/breakdancer

Date: May 17, 2016

Version: 1.2

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: cd src; make

Options:

Source Download: https://github.com/marbl/canu/releases

Date: Sept 29, 2016

Version: CASHX_2.3

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ./configure --prefix=/usr; make; make install

Options:

Source Download: https://www.danforthcenter.org/scientists-research/principal-investigators/james-carrington/resources

Date: June 30, 2016

Version: 1.9.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux; make; make install

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: https://sourceforge.net/projects/cdbfasta/

Date: Jan 25, 2017

Version: 2.5

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make; make install

Options:

Source Download: http://korflab.ucdavis.edu/datasets/cegma/

Date: Aug 25, 2016

Version: 1.0.9

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make

Options:

Source Download: http://bioinformatics.hungry.com/clearcut/

Date: June 21, 2016

Version: 3.4.3

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://www.cmake.org/files/v3.4/cmake-3.4.3.tar.gz

Date: May 23, 2016

Version: conifer_v0.2.2

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://conifer.sourceforge.net/

Date: Jan 17, 2017

Version: Corset-version-1.05

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ./configure --prefix=/local/cluster/Corset-version-1.05 --with-bam_inc=/local/cluster/samtools-0.1.19

Options:

Source Download: https://github.com/Oshlack/Corset/wiki/Download

Date: August 25, 2016

Version: 6.1.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://projects.coin-or.org/Csdp/

Date:

Version:

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Date: April 28, 2016

Version: 2.2.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: http://cole-trapnell-lab.github.io/cufflinks/install/

Date: Feb 27, 2017

Version: 1.8.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: python setup.py install

Options:

Source Download: https://pypi.python.org/pypi/cutadapt/1.8.1

Date: May 23, 2016

Version: 8

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://opencvblobslib.github.io/opencvblobslib/

Date: July 14, 2016

Version: 0.8.2

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: github.com/msettles/dbcAmplicons

Date: Jan 25, 2017

Version: 0.8.26

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: Benjamin Buchfink from Diamond group compiled this to work on the power.

Options:

Source Download: https://github.com/bbuchfink/diamond

Date: Jun 24, 2016

Version: 52488

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://software.broadinstitute.org/software/discovar/blog/?page_id=98

Date: May 23, 2016

Version: drFAST-1.0.0.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: need to have zlib-static

Options:

Source Download: http://drfast.sourceforge.net/

Date: July 17, 2016

Version: 2.1.11

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://sourceforge.net/projects/egglib/files/

Date: March 21, 2016

Version: 6.5.7

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ./configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options:

Source Download: http://emboss.sourceforge.net/download/

Date: August 1, 2016

Version: 2.2.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: https://sourceforge.net/u/djinnome/jamg/ci/47152a01077445af52726d76270e60bb360bb2f2/tree/3rd_party/exonerate-2.2.0/

Date:

Version:

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Date: March 29, 2017

Version: 0.0.14

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig:(libgtex install path)/lib/pkgconfig; ./configure --build=ppc64; make; make install

Options:

Source Download: http://hannonlab.cshl.edu/fastx_toolkit/download.html

Date: July 21, 2016

Version: 3.1.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://ffmpeg.org/releases/

Date: July 19, 2016

Version: v1.0.2-33-gdbb6160

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://github.com/ekg/freebayes/releases/tag/v1.0.2

Date:

Version:

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Date: March 08, 2018

Version: gapfiller-2.1.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ./configure LIBS="-lz" --build=ppc64

Options:

Source Download: https://sourceforge.net/p/gapfiller/wiki/Home/

Date:

Version:

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Date: January 30, 2017

Version:

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://exon.gatech.edu/Genemark/license_download.cgi

Date: Aug 24, 2016

Version: 3.5

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: install java

Options:

Source Download: https://software.broadinstitute.org/gatk/download/

Date: July 15, 2016

Version: 4.60

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: https://ftp.gnu.org/gnu/glpk/

Date: March 25, 2016

Version: 5.1.2

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://www.gromacs.org/Downloads

Date: July 15, 2016

Version: 2.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://ftp.gnu.org/gnu/gsl/

Date:

Version:

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Date: July 20, 2016

Version: 8.0-3.10

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://sourceforge.net/projects/jdk7src/

Date: July 11, 2016

Version: 1.1.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/

Date:

Version:

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Date: April 13, 2016

Version: 5.18-57.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://github.com/ebi-pf-team/interproscan/wiki/HowToDownload

Date: August 25, 2016

Version: 1.14.8

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://sourceforge.net/projects/staden/files/io_lib/

Date: March 23, 2017

Version: 4.2.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ./configure; make; make install

Options:

Source Download: http://mcmc-jags.sourceforge.net/

Date: July 20, 2016

Version: 8.0-3.10

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://sourceforge.net/projects/jdk7src/

Date: July 20, 2016

Version: 0.5.0-dev

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options: The Julia group worked with the CGRB to compile a version of Julia for the IBM Power8.

Source Download: https://github.com/JuliaLang/julia

Date: June 21, 2016

Version: 0.43.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://pachterlab.github.io/kallisto/starting

Date: July 8, 2016

Version: 746

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://last.cbrc.jp/last-746.zip

Date: March 29, 2017

Version: 0.7

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ./configure --build=ppc64; make; make install

Options:

Source Download: http://hannonlab.cshl.edu/fastx_toolkit/download.html

Date: May 17, 2016

Version: 2.0.10

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://github.com/taoliu/MACS

Date: May 17, 2016

Version: 6.956-with-extensions

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make clean; make; su; make install

Options:

Comments:

Source Download: http://mafft.cbrc.jp/alignment/software/mafft-6.956-with-extensions-src.tgz

Date: Jan 26, 2017

Version: 2.31

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: install needed perl modules

Options:

Source Download: http://www.yandell-lab.org/software/maker.html

Date: May 23, 2016

Version: MaM-1.4.2

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make

Options:

Source Download: http://mam-bio.sourceforge.net/Home

Date: Oct 9, 2016

Version: 2.0.6

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: python setup.py

Options:

Source Download: https://github.com/ginolhac/mapDamage

Date: March 24, 2017

Version: 3.2.2_RC1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: edit the files global-1/PacBio/include/charb.hpp and comment out the int3 line like this '// asm("int3;")'; edit the files global-1/SuperReads/include/charb.hpp and comment out the int3 line like this '// asm("int3;")'; ./install.sh

Options:

Source Download: http://www.genome.umd.edu/masurca.html

Date: April 19, 2017

Version: v1.1.1-2-g02102e1

Operating System: Centos 7

OS Version: 3.10.0-514.2.2.el7.ppc64le

Setup: make disablempopcnt=1

Options:

Source Download: https://github.com/voutcn/megahit

Date: Aug 26, 2016

Version: 1.8

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: perl -c ./MITObim.pl

Options:

Source Download: https://github.com/chrishah/MITObim

Date: June 20, 2016

Version: 1.39.3

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://github.com/mothur/mothur/releases

Date: May 23, 2016

Version: mrsfast-v3.4.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make

Options:

Source Download: http://sfu-compbio.github.io/mrsfast/

Date: July 17, 2016

Version: 5

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: http://fletcherpenney.net/2015/11/mmd_5.0.0_released

Date: March 24, 2017

Version: 3.23

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make

Options:

Source Download: http://mummer.sourceforge.net/

Date: March 1, 2017

Version: 2.2

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ./configure; make; make install

Options:

Source Download: http://mvapich.cse.ohio-state.edu/register/

Date: March 15, 2016

Version: 2.6.0+

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/

Date: August 24, 2016

Version: 2.2.28

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/rmblast/2.2.28/

Date: May 23, 2016

Version: 1.0.2

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ls -1| grep cpp | sed 's/.cpp//g' | xargs -i00 g++ 00.cpp -o 00; gcc -std=c99 sortString.c -o sortString; gcc fs-fa.c -o fs-fa

Options: There is no makefile so you will need to compile everything by hand.

Source Download: https://sourceforge.net/projects/novelseq/files/?source=navbar

Date: Jun 30, 2016

Version: 1.11.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: python setup.py

Options:

Source Download: http://www.scipy.org/scipylib/download.html

Date: June 17, 2016

Version: 3.1.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://opencv.org/downloads.html

Date: July 15, 2016

Version: 2.10

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: https://github.com/neufeld/pandaseq/releases

Date: Feb 08, 2016

Version: v7.6

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: Needs Tk.pm

Options:

Source Download: http://eichlerlab.gs.washington.edu/jeff/parasight/index.html

Date: March 22, 2017

Version: 0.9.10

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: autoconf; ./configure; make; make install

Options: Edit the src/pear-pt.c and add "#include <stdarg.h>" to the top include section

Source Download: http://sco.h-its.org/exelixis/web/software/pear/

Date: March 22, 2017

Version: pgilinux-2016-1610-ppc64le

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ./install

Options:

Source Download: http://www.pgroup.com/products/community.htm

Date: May 23, 2016

Version: 2.2.3

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: sourceforge.net/projects/primer3/files/primer3/2.2.3/

Date: March 15, 2017

Version: 2.6.3

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make

Options:

Source Download: https://github.com/hyattpd/Prodigal

Date: June 30, 2016

Version: 0.7.14

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://sourceforge.net/projects/pyml/

Date: March 21, 2016

Version: 2.22

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://github.com/zhaoyanswill/RAPSearch2

Date: June 30, 2016

Version: 2.12

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download:

Date: Jan 26, 2017

Version: 4.0.6

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://www.repeatmasker.org/RMDownload.html

Date: June 30, 2016

Version: 1.4.2

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://sourceforge.net/projects/rkhunter/files/

Date: Feb 27, 2017

Version: 1.3.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make

Options:

Source Download: https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz

Date: June 28, 2016

Version: 2.2.3

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: https://www.ruby-lang.org/en/news/2015/08/18/ruby-2-2-3-released/

Date:

Version:

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Date: August 26, 2016

Version: 2.1.14

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://sourceforge.net/projects/sequenceread/files/sequenceread/2.1.4/

Date: April 20, 2017

Version: 1.0

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make

Options:

Source Download: https://github.com/guo-xuan/Sipros-Ensemble

Date: May 23, 2016

Version: 1.2.09

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://korflab.ucdavis.edu/software.html

Date: May 23, 2016

Version: 2.04-r240

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://sourceforge.net/projects/soapdenovo2/

Date: May 23, 2016

Version: 1.2.09

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://arc.liv.ac.uk/downloads/SGE/releases/

Date: February 15, 2016

Version: 2.0.3

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://github.com/btgraham/SparseConvNet

Date: June 16, 2016

Version: 2.0.3

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: https://github.com/sparsehash/sparsehash/releases

Date: May 23, 2016

Version: v0.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: sh Make.sh

Options:

Source Download: http://splitread.sourceforge.net/

Date: Feb 20, 2017

Version: 1.3.3

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make

Options:

Source Download: https://ccb.jhu.edu/software/stringtie/#install

Date: June 15, 2016

Version: 4.0.6

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: http://download.osgeo.org/libtiff/

Date: March 16, 2016

Version: 2.1.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: http://ccb.jhu.edu/software/tophat/downloads/

Date: Feb 27, 2017

Version: 0.27

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make; make install

Options:

Source Download: https://github.com/timflutre/trimmomatic

Date: June 20, 2016

Version: r20140717

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make

Options:

Source Download: https://github.com/trinityrnaseq/trinityrnaseq.git

Date: August 24, 2016

Version: 1.3.1

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz

Date: May 23, 2016

Version: 1.2.09

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://www.linuxfromscratch.org/blfs/view/svn/general/unzip.html

Date: May 23, 2016

Version: v0.04

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: make inside the clustering and selection directories

Options:

Source Download: https://sourceforge.net/projects/variationhunter/files/

Date: June 29, 2016

Version: 0.1.14

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-ppc64le-redhat-linux/cloog-install --enable-gnu-indirect-function --enable-secureplt --with-long-double-128 --enable-targets=powerpcle-linux --disable-multilib --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Options: --with-cpu-64=power7 --with-tune-64=power8 --build=ppc64le-redhat-linux

Source Download: https://sourceforge.net/projects/vcftools/files/

Date: May 23, 2016

Version: 1.2.09

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.09.tgz

Date: June 22, 2016

Version: vsearch-2.4.0-linux-ppc64le

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup: Download Binaries

Options:

Source Download: https://github.com/torognes/vsearch/releases/tag/v2.4.0

Date: August 29, 2016

Version: 1.2.8

Operating System: Centos 7

OS Version: 3.10.0-327.4.4.el7.ppc64le

Setup:

Options:

Source Download: http://www.zlib.net/fossils/

R Packages

    Python Packages

    • -ipap11helper (0.1)
    • avro (1.8.0)
    • backports.shutil-get-terminal-size (1.0.0)
    • backports.ssl-match-hostname (3.4.0.2)
    • Beaker (1.5.4)
    • biom-format (2.1.5)
    • biopython (1.66)
    • biopython (1.66)
    • blivet (0.61.15.37)
    • Brlapi (0.6.0)
    • burrito (0.9.1)
    • bz2file (0.98)
    • cffi (0.8.6)
    • chardet (2.2.1)
    • click (6.6)
    • cogent (1.5.3)
    • configobj (4.7.2)
    • configobj (5.0.6)
    • configshell-fb (1.1.18)
    • coverage (3.6b3)
    • cryptography (0.8.2)
    • cupshelpers (1.0)
    • cutadapt (1.8.1)
    • cycler (0.10.0)
    • cycler (0.10.0)
    • Cython (0.23.4)
    • Cython (0.23.4)
    • dask (0.10.2)
    • dask (0.10.2)
    • decorator (3.4.0)
    • decorator (4.0.10)
    • DendroPy (4.1.0)
    • DendroPy (4.1.0)
    • di (0.3)
    • dnspython (1.12.0)
    • ecdsa (0.13)
    • enum34 (1.0.4)
    • ethtool (0.8)
    • Fabric (1.10.2)
    • firstboot (19.5)
    • franklin (1.4.0)
    • freeipa (2.0.0a0)
    • fros (1.0)
    • functools32 (3.2.3.post2)
    • future (0.15.2)
    • gdata (2.0.18)
    • h5py (2.5.0)
    • iniparse (0.4)
    • initial-setup (0.3.9.30)
    • iotop (0.6)
    • ipaplatform (4.2.0)
    • ipapython (4.2.0)
    • IPy (0.75)
    • ipython (4.2.1)
    • ipython-genutils (0.1.0)
    • iso8601 (0.1.11)
    • javapackages (1.0.0)
    • Jinja2 (2.8)
    • jsonpointer (1.9)
    • jsonschema (2.5.1)
    • Keras (0.3.2)
    • kerberos (1.1)
    • kitchen (1.1.1)
    • kmod (0.1)
    • langtable (0.0.31)
    • lxml (3.2.1)
    • M2Crypto (0.21.1)
    • MACS2 (2.0.10.9132012)
    • Mako (0.8.1)
    • mapdamage (2.0)
    • MarkupSafe (0.11)
    • matplotlib (1.5.1)
    • matplotlib (1.5.1)
    • mercurial (2.6.2)
    • MicrobeCensus (1.0.7)
    • MySQL-python (1.2.3)
    • natsort (3.5.6)
    • netaddr (0.7.5)
    • networkx (1.11)
    • networkx (1.11)
    • nose (1.3.0)
    • ntplib (0.3.2)
    • numpy (1.10.4)
    • numpy (1.10.4)
    • openlmi (0.5.0)
    • pandas (0.18.1)
    • paramiko (1.16.0)
    • Paste (1.7.5.1)
    • pathlib2 (2.1.0)
    • pbcommand (0.3.21)
    • pbcommand (0.3.21)
    • pbcore (1.2.8)
    • pbcoretools (0.1.7)
    • pbreports (3.1.1)
    • pbsmrtpipe (0.36.6)
    • pcp (1.0)
    • perf (0.1)
    • pexpect (4.2.0)
    • pickleshare (0.7.2)
    • Pillow (3.3.0)
    • Pillow (3.3.0)
    • pip (8.0.3)
    • pip (8.1.2)
    • ply (3.4)
    • policycoreutils-default-encoding (0.1)
    • powerpcAMS (1.2.1)
    • ptyprocess (0.5.1)
    • pyasn1 (0.1.6)
    • pycparser (2.14)
    • pycrypto (2.6.1)
    • pycups (1.9.63)
    • pycurl (7.19.0)
    • pydot (1.0.2)
    • pygobject (3.14.0)
    • pygpgme (0.3)
    • pyinotify (0.9.4)
    • pykickstart (1.99.66.6)
    • pyliblzma (0.5.3)
    • pynast (1.2.2)
    • pyOpenSSL (0.13.1)
    • pyparsing (1.5.7)
    • pyparsing (2.1.0)
    • pyparted (3.9)
    • pyqi (0.3.2)
    • pysam (0.8.4)
    • pysam (0.9.0)
    • python-augeas (0.5.0)
    • python-dateutil (1.5)
    • python-dateutil (2.5.0)
    • python-default-encoding (0.1)
    • python-dmidecode (3.10.13)
    • python-ldap (2.4.15)
    • python-meh (0.25.2)
    • python-nss (0.16.0)
    • python-yubico (1.2.3)
    • pytz (2012d)
    • pytz (2016.1)
    • pyudev (0.15)
    • pyusb (1.0.0b1)
    • pywbem (0.7.0)
    • pyxattr (0.5.1)
    • PyYAML (3.11)
    • qcli (0.1.1)
    • qiime-default-reference (0.1.3)
    • qrcode (5.0.1)
    • requests (2.9.1)
    • rtslib-fb (2.1.57)
    • scikit-image (0.12.3)
    • scikit-image (0.12.3)
    • scipy (0.17.0)
    • scipy (0.17.1)
    • sckdump (2.0.13)
    • screed (0.9)
    • seobject (0.1)
    • sepolicy (1.1)
    • setroubleshoot (1.1)
    • setuptools (0.9.8)
    • setuptools (24.0.2)
    • simplegeneric (0.8.1)
    • simuPOP (1.0.6)
    • six (1.9.0)
    • six (1.10.0)
    • slip (0.4.0)
    • slip.dbus (0.4.0)
    • SpliceGrapher (0.2.4)
    • SpliceGrapher (0.2.4)
    • SSSDConfig (1.13.0)
    • targetcli-fb (2.1.fb41)
    • Tempita (0.5.1)
    • Theano (0.8.0.dev0)
    • toolz (0.8.0)
    • toolz (0.8.0)
    • traitlets (4.2.2)
    • urlgrabber (3.10)
    • urwid (1.1.1)
    • virtualenv (14.0.6)
    • xmlbuilder (1.0)
    • yum-langpacks (0.4.2)
    • yum-metadata-parser (1.1.4)

Programs

  • 2to3
  • a2m2selex.pl
  • aaindexextract
  • aalookup_unit_test
  • aascan_unit_test
  • abiview
  • ABYSS
  • abyss-align
  • abyss-bloom
  • abyss-bloom-dist.mk
  • abyss-bowtie
  • abyss-bowtie2
  • abyss-bwa
  • abyss-bwamem
  • abyss-bwasw
  • abyss-db-csv
  • abyss-db-txt
  • abyss-dida
  • abyss-fac
  • abyss-fatoagp
  • abyss-filtergraph
  • abyss-fixmate
  • abyss-fixmate-ssq
  • abyss-gapfill
  • abyss-gc
  • abyss-index
  • abyss-junction
  • abyss-kaligner
  • abyss-layout
  • abyss-longseqdist
  • abyss-map
  • abyss-map-ssq
  • abyss-mergepairs
  • abyss-overlap
  • abyss-paired-dbg
  • abyss-pe
  • abyss-samtoafg
  • abyss-scaffold
  • abyss-sealer
  • abyss-tabtomd
  • abyss-todot
  • abyss-tofastq
  • acdc
  • acdgalaxy
  • acdlog
  • acdpretty
  • acdtable
  • acdtrace
  • acdvalid
  • ace2sam
  • adapter_xml
  • addsingle
  • AddUnibaseJunctions
  • add_ambiguous_counts.py
  • add_custom_gene.py
  • AdjList
  • AffineAlign
  • agrep
  • align.c
  • align.o
  • aligncopy
  • aligncopypair
  • alignio.c
  • alignio.o
  • AlignPairsToFasta
  • AlignReads
  • AlignUnibasesToRef
  • align_format_unit_test
  • align_main.c
  • AllPathsCache.pm
  • AllPathsReport
  • aln2wig
  • amplicon_analysis_consensus_report
  • amplicon_analysis_input_report
  • amplicon_analysis_timing_report
  • analyze_exon-exon_mappings.py
  • analyze_splits_sam.py
  • analyze_star_chimeric.py
  • annotate
  • annotateBed
  • annotate_variation.pl
  • antigenic
  • append_sff
  • ApplyAssemblyEdits
  • ApplyGapPatches
  • ArachneArgs.pm
  • Archaea-BHB-noncan.cm
  • ArrayList.pm
  • ArrayListIterator.pm
  • arrow
  • ass3.pl
  • ass3_single_threaded.pl
  • AssemblyAccuracy
  • AssemblyCoverage
  • assemblyget
  • ass_to_html.pl
  • augustus
  • avro
  • backtranambig
  • backtranseq
  • bam2fastx
  • bamleftalign
  • bamSieve
  • bamToBed
  • bamToFastq
  • bam_merge
  • banana
  • barcode_report
  • bazel
  • bcftools
  • bdbloader_unit_test
  • bdf2gdfont.pl
  • bdf2gdfont.PLS
  • bdftogd
  • bed12ToBed6
  • bedpeToBam
  • bedToBam
  • bedToIgv
  • bedtools
  • bed_to_juncs
  • bet_to_gff.pl
  • bgzip
  • bgzip.org
  • bib
  • bib-admin
  • bib-test
  • bib2xml
  • biblatex2xml
  • BigMap
  • bioawk
  • biom
  • biopython_version.py
  • biosed
  • bl2seq
  • bl2seq_unit_test
  • blast2sam.pl
  • blastall
  • blastclust
  • blastdbcheck
  • blastdbcmd
  • blastdbcp
  • blastdb_aliastool
  • blastdb_format_unit_test
  • blastdiag_unit_test
  • blastengine_unit_test
  • blastextend_unit_test
  • blastfilter_unit_test
  • blasthits_unit_test
  • blastinput_unit_test
  • blastn
  • blastoptions_unit_test
  • blastp
  • blastpgp
  • blastsetup_unit_test
  • blastx
  • blast_formatter
  • blast_format_unit_test
  • blast_services_unit_test
  • blast_unit_test
  • blat-filter-fusion.py
  • blat-filter-fusion.sh
  • blat_parallel.py
  • bmp2tiff
  • bogart
  • bogus
  • bootstrap.py
  • bowtie
  • bowtie2
  • bowtie2-align-l
  • bowtie2-align-s
  • bowtie2-build
  • bowtie2-build-l
  • bowtie2-build-s
  • bowtie2-inspect
  • bowtie2-inspect-l
  • bowtie2-inspect-s
  • bowtie2sam.pl
  • bp_aacomp.pl
  • bp_biofetch_genbank_proxy.pl
  • bp_bioflat_index.pl
  • bp_biogetseq.pl
  • bp_blast2tree.pl
  • bp_bulk_load_gff.pl
  • bp_chaos_plot.pl
  • bp_classify_hits_kingdom.pl
  • bp_composite_LD.pl
  • bp_das_server.pl
  • bp_dbsplit.pl
  • bp_download_query_genbank.pl
  • bp_extract_feature_seq.pl
  • bp_fastam9_to_table.pl
  • bp_fast_load_gff.pl
  • bp_fetch.pl
  • bp_filter_search.pl
  • bp_find-blast-matches.pl
  • bp_flanks.pl
  • bp_gccalc.pl
  • bp_genbank2gff.pl
  • bp_genbank2gff3.pl
  • bp_generate_histogram.pl
  • bp_heterogeneity_test.pl
  • bp_hivq.pl
  • bp_hmmer_to_table.pl
  • bp_index.pl
  • bp_load_gff.pl
  • bp_local_taxonomydb_query.pl
  • bp_make_mrna_protein.pl
  • bp_mask_by_search.pl
  • bp_meta_gff.pl
  • bp_mrtrans.pl
  • bp_mutate.pl
  • bp_netinstall.pl
  • bp_nexus2nh.pl
  • bp_nrdb.pl
  • bp_oligo_count.pl
  • bp_pairwise_kaks.pl
  • bp_parse_hmmsearch.pl
  • bp_process_gadfly.pl
  • bp_process_sgd.pl
  • bp_process_wormbase.pl
  • bp_query_entrez_taxa.pl
  • bp_remote_blast.pl
  • bp_revtrans-motif.pl
  • bp_search2alnblocks.pl
  • bp_search2BSML.pl
  • bp_search2gff.pl
  • bp_search2table.pl
  • bp_search2tribe.pl
  • bp_seqconvert.pl
  • bp_seqcut.pl
  • bp_seqfeature_delete.pl
  • bp_seqfeature_gff3.pl
  • bp_seqfeature_load.pl
  • bp_seqpart.pl
  • bp_seqret.pl
  • bp_seqretsplit.pl
  • bp_seq_length.pl
  • bp_seq_select.pl
  • bp_split_seq.pl
  • bp_sreformat.pl
  • bp_taxid4species.pl
  • bp_taxonomy2tree.pl
  • bp_translate_seq.pl
  • bp_tree2pag.pl
  • bp_unflatten_seq.pl
  • breakdancer-max
  • breakReads
  • breakReads.c
  • BreakUnlinkedAssisted
  • btwisted
  • buildGraph
  • BuildUnipathLinkGraphsLG
  • build_classifiers.py
  • build_ig.py
  • build_main.c
  • build_mod.pl
  • build_report_fusions_map.py
  • build_report_fusions_psl.py
  • build_summary.py
  • busy-nodes
  • cachedas
  • cachedbfetch
  • cacheebeyesearch
  • cacheensembl
  • CacheGroups.pl
  • CacheLibs.pl
  • CacheReadsMerge
  • CacheToAllPathsInputs.pl
  • CacheToReads.pl
  • cai
  • calc_introns_from_gtf.pl
  • calProbMinEditRead
  • canu
  • canu.defaults
  • cashx_formatDB
  • cashx_searchDB
  • cashx_verifyDB
  • ccmake
  • ccs_report
  • cdbfasta
  • cdbyank
  • cds-trainer.pl
  • cegma
  • cegma2zff
  • chado2gff3
  • ChangeLibraryStats
  • chaos
  • charge
  • checktrans
  • checkversion.pl
  • check_modules.pl
  • chips
  • cifar10
  • cirdna
  • classify_sites.py
  • CleanAssembly
  • CleanCorrectedReads
  • CleanLongReadPatches
  • clean_bed.py
  • clearcut
  • clip_quality.py
  • clm
  • clmformat
  • closestBed
  • CloseUnipathGaps
  • clusterBed
  • clxdo
  • cmake
  • CmpSeq
  • codcmp
  • codcopy
  • coderet
  • codes.english
  • coding_change.pl
  • combineMUMs
  • CommonPather
  • compare
  • CompileAssemblyReport.pl
  • complement
  • complementBed
  • completeness
  • compress-reads-ids.py
  • compress_gtf
  • compseq
  • concatenate.py
  • configuration.py
  • config_data
  • conifer.py
  • ConnectScaffolds
  • cons
  • consambig
  • Consensus
  • consensusFinder
  • contig_to_chr_coords
  • contrafoldwrap
  • convert0.6.pl
  • convert0.6.README
  • convert0.8.pl
  • convert0.8.README
  • convert2annovar.pl
  • convert2blastmask
  • convert2ReadTo4Read.py
  • ConvertToFastbQualb.pl
  • convertToInvLRProbMinEditDist
  • convert_models.py
  • convert_pairs_symbols.py
  • convert_trace
  • copac2xml
  • COPYING
  • copylink
  • copymat
  • CorrectLongReads
  • correctOverlaps
  • corset
  • corset_fasta_ID_changer
  • countlen
  • covels-SE
  • coverageBed
  • coves-SE
  • cpack
  • cpgplot
  • cpgreport
  • cram_dump
  • cram_index
  • cram_size
  • crc32
  • createFalconSenseInputs
  • createfontdatachunk.py
  • CreateLookupTab
  • createScoreMatrix
  • CrossmatchSearchEngine.pm
  • CrossOut
  • csdp
  • ctest
  • cuffcompare
  • cuffdiff
  • cufflinks
  • cufflinks2gff3
  • cuffmerge
  • cuffnorm
  • cuffquant
  • curve2hints
  • cusp
  • cutadapt
  • cutgextract
  • cutseq
  • cvtbdf.pl
  • cygdb
  • cython
  • cythonize
  • dan
  • DAssembler
  • dataset
  • dataset.py
  • datatool
  • DateRepeats
  • dbcAmplicons
  • dbiblast
  • dbifasta
  • dbiflat
  • dbigcg
  • dbmalloc.h
  • dbtell
  • dbviterbi.c
  • dbviterbi.o
  • dbxcompress
  • dbxedam
  • dbxfasta
  • dbxflat
  • dbxgcg
  • dbxobo
  • dbxreport
  • dbxresource
  • dbxstat
  • dbxtax
  • dbxuncompress
  • dead-nodes
  • debug.c
  • debug.o
  • DeCypherSearchEngine.pm
  • degapseq
  • delta-filter
  • deltablast
  • delta_unit_test
  • demux.pl
  • density
  • descseq
  • DFAM.pm
  • DFAMRecord.pm
  • diamond
  • diffseq
  • DiscovarDeNovo
  • DisplayLibraryStats
  • DisplayLocs
  • DistanceEst
  • DistanceEst-ssq
  • distmat
  • disttbfast
  • dnadiff
  • dndblast
  • dndfast7
  • dndpre
  • dndpre2
  • DomainFinder3
  • dotmatcher
  • dotpath
  • dottup
  • dreg
  • drfast
  • drfinddata
  • drfindformat
  • drfindid
  • drfindresource
  • drget
  • drtext
  • Dsignal
  • DumpHyper
  • DupMasker
  • dustmasker
  • dvtditr
  • easy_install
  • easy_install-2.7
  • ebi2xml
  • ecoPrimers
  • edamdef
  • edamhasinput
  • edamhasoutput
  • edamisformat
  • edamisid
  • edamname
  • EdgeInfo
  • edialign
  • EfastaToFasta
  • EGC.0
  • EGC.1
  • EGC.2
  • EGC.3
  • EGC.4
  • EGC.5
  • EGC.6
  • EGC.9
  • EGC.10
  • EGC.11
  • EGC.12
  • EGC.13
  • EGC.14
  • EGC.15
  • EGC.16
  • EGC.21
  • EGC.22
  • EGC.23
  • EGC.index
  • EGC.txt
  • einverted
  • embossdata
  • embossupdate
  • embossversion
  • emit.c
  • emit.o
  • emit_main.c
  • emma
  • emowse
  • end2xml
  • endx2xml
  • enhancer.py
  • enlarge_genes.py
  • entret
  • epestfind
  • eprimer3
  • eprimer32
  • equicktandem
  • erateEstimate
  • erb
  • ErrorCorrectJump
  • ErrorCorrectReads.pl
  • errorEstimate
  • esd2esi
  • ESELC.cm
  • ESELCinf-c.cm
  • est2genome
  • estimate-mer-threshold
  • ests_to_splicegraph.py
  • etandem
  • etraining
  • eufindtRNA
  • eufind_const.h
  • eufind_main.c
  • eufind_main.o
  • EvalScaffolds
  • EvaluateCorrectedPairs
  • EvaluateGaps
  • evaluator
  • EvalUnipathLinkGraphs
  • events5
  • exact-tandems
  • example
  • exonerate
  • exonerate-server
  • exonpairs
  • expandCols
  • explode.py
  • export2sam.pl
  • external_to_gff.pl
  • extractalign
  • extractfeat
  • extractseq
  • extract_fastq
  • extract_fusion_genes.py
  • extract_qual
  • extract_reads_ids.py
  • extract_seq
  • extract_short_reads.py
  • extract_transcripts.py
  • f2cl
  • f2py
  • fa2fq
  • fa2fq.o
  • FakeQualb
  • falcon-task
  • falcon_sense
  • fast-dbviterbi.c
  • fast-dbviterbi.o
  • fasta2esd
  • Fasta2Fastb
  • fasta2gsi.pl
  • fasta2reads.py
  • fastaannotatecdna
  • fastachecksum
  • fastaclean
  • fastaclip
  • fastacmd
  • fastacomposition
  • FastaDB.pm
  • fastadiff
  • fastaexplode
  • fastafetch
  • fastaFromBed
  • fastahardmask
  • fastaindex
  • fastalength
  • fastanrdb
  • fastaoverlap
  • fastareformat
  • fastaremove
  • fastarevcomp
  • fastasoftmask
  • fastasort
  • fastasplit
  • fastasubseq
  • FastaToEfasta
  • fastatranslate
  • fastavalidcds
  • fasta_checker.pl
  • fasta_clipping_histogram.pl
  • fasta_formatter
  • fasta_merge
  • fasta_nucleotide_changer
  • fasta_tool
  • Fastb
  • Fastb2Fasta
  • fastBlockSearch
  • FastbMerge
  • FastbQualbToFastq
  • FastbQualbTrimReverse
  • FastbStats
  • fastmodelmaker.c
  • fastmodelmaker.o
  • fastq-interleave
  • fastq2fasta.py
  • fastqAnalyze
  • fastqdeloea
  • fastqdeloea.c
  • fastqSample
  • fastqSimulate
  • fastqSimulate-sort
  • FastqToFastbQualb
  • fastq_b2n.py
  • fastq_masker
  • fastq_quality_boxplot_graph.sh
  • fastq_quality_converter
  • fastq_quality_filter
  • fastq_quality_trimmer
  • fastq_to_fasta
  • FastTree
  • FastTreeMP
  • fastx_artifacts_filter
  • fastx_barcode_splitter.pl
  • fastx_clipper
  • fastx_collapser
  • fastx_nucleotide_distribution_graph.sh
  • fastx_nucleotide_distribution_line_graph.sh
  • fastx_quality_stats
  • fastx_renamer
  • fastx_reverse_complement
  • fastx_trimmer
  • fastx_uncollapser
  • fathom
  • fax2ps
  • fax2tiff
  • FC
  • fc_actg_coordinate
  • fc_actg_coordinate.py
  • fc_calc_cutoff
  • fc_consensus
  • fc_consensus.py
  • fc_contig_annotate
  • fc_contig_annotate.py
  • fc_ctg_link_analysis
  • fc_ctg_link_analysis.py
  • fc_dedup_a_tigs
  • fc_dedup_a_tigs.py
  • fc_fasta2fasta
  • fc_graph_to_contig
  • fc_graph_to_contig.py
  • fc_graph_to_utgs
  • fc_graph_to_utgs.py
  • fc_ovlp_filter
  • fc_ovlp_filter.py
  • fc_ovlp_stats
  • fc_ovlp_stats.py
  • fc_ovlp_to_graph
  • fc_ovlp_to_graph.py
  • fc_run
  • fc_run.py
  • fc_run1
  • featcopy
  • featmerge
  • featreport
  • feattext
  • ffmpeg
  • ffplay
  • ffprobe
  • ffserver
  • filehashsha.pl
  • FILES
  • fill-aa
  • fill-an-ac
  • fill-fs
  • fill-ref-md5
  • FillFragments
  • filterCorrectionOverlaps
  • filterfa
  • filterfa.o
  • FilterPrunedReads
  • filter_blat
  • filter_blat.o
  • filter_contigs
  • filter_contigs.o
  • filter_stats
  • filter_stats_xml
  • filter_subread
  • filter_subread_summary
  • Finalevents_v5.c
  • findErrors
  • FindErrors
  • findErrors-Dump
  • findkm
  • FindUnipathGaps
  • find_fusion_genes_map.py
  • find_fusion_genes_psl.py
  • find_homolog_genes.py
  • find_splice_forms.py
  • fingerPRINTScan
  • fix.py
  • FixAssemblyBaseErrors
  • FixLocal
  • FixPrecompute
  • FixSomeIndels
  • fix_map_ordering
  • fix_unresolved.py
  • flankBed
  • FlattenHKP
  • forge
  • formatdb
  • formatrpsdb
  • FormPath
  • fq2fa
  • fq2fa.o
  • fragments_fusion_genes.py
  • fragment_fastq.py
  • freak
  • freebayes
  • fs-fa
  • funcs.h
  • funzip
  • fusioncatcher
  • fusioncatcher-batch
  • fusioncatcher-batch.py
  • fusioncatcher-build
  • fusioncatcher-build.py
  • fusioncatcher.py
  • futurize
  • fuzznuc
  • fuzzpro
  • fuzztran
  • GapFiller
  • GapFiller_debug
  • gapinfo_unit_test
  • gaps
  • garnier
  • gatekeeperCreate
  • gatekeeperDumpFASTQ
  • gatekeeperDumpMetaData
  • gatekeeperPartition
  • gc
  • gcode.cilnuc
  • gcode.echdmito
  • gcode.invmito
  • gcode.othmito
  • gcode.vertmito
  • gcode.ystmito
  • gc_distr.pl
  • geecee
  • gem
  • gencode_singleton_unit_test
  • geneid-train
  • genemark_gtf2gff3
  • genePredToBed
  • generateCorrectionLayouts
  • GenerateMapUnibasesToContigs
  • generate_18cancers.py
  • generate_1000genomes.py
  • generate_adjacent_genes.py
  • generate_banned.py
  • generate_bodymap2.py
  • generate_chrom_lens.py
  • generate_enlarge.py
  • generate_exon-exon_junctions.py
  • generate_exons.py
  • generate_gene-gene_junctions.py
  • generate_genes.py
  • generate_genes_symbols.py
  • generate_genes_with_no_proteins.py
  • generate_gliomas.py
  • generate_healthy.py
  • generate_hpa.py
  • generate_known.py
  • generate_known_junctions.py
  • generate_labels_descriptions.py
  • generate_nontumor.py
  • generate_oesophagus.py
  • generate_overlapping_genes.py
  • generate_pairs_pseudogenes.py
  • generate_predicted_junctions.py
  • generate_putative_sequences.py
  • generate_roc.py
  • generate_rrna_unit.py
  • generate_splice_site_data.py
  • generate_tcga.py
  • generate_transcripts.py
  • gene_info_reader
  • gene_info_unit_test
  • gene_model_to_splicegraph.py
  • genomeCoverageBed
  • GenomeReadLocsLG
  • GenomeToPaths
  • genome_map
  • getFinalevents.sh
  • getlag
  • getopt.c
  • getopt.o
  • getorf
  • getorf.acd
  • getOverlap
  • get_biotypes.py
  • get_cacg.py
  • get_celllines.py
  • get_cgp.py
  • get_chimerdb2.py
  • get_chimerdb3.py
  • get_comment
  • get_conjoing.py
  • get_cosmic.py
  • get_dgd.py
  • get_exons_positions.py
  • get_gencode.py
  • get_genes_descriptions.py
  • get_genome.py
  • get_good_pairs.py
  • get_gtex.py
  • get_gtf.py
  • get_hla.py
  • get_mtrna.py
  • get_noncancer.py
  • get_pancreases.py
  • get_paralogs.py
  • get_phix174.py
  • get_prostates.py
  • get_refseq.py
  • get_refseq_ensembl.py
  • get_rrna.py
  • get_sequence_from_GTF.pl
  • get_synonyms.py
  • get_ticdb.py
  • get_trna.py
  • get_ucsc.py
  • get_viruses.py
  • gff3_merge
  • gffread
  • gffToBed
  • gffToVcf
  • Gibbs3
  • gif2h5
  • gif2tiff
  • gifmaker.py
  • glpsol
  • gm
  • gm.pl
  • gmes
  • gmes_petap.pl
  • gmhmme3
  • gmhmmp
  • gmhmmp.pl
  • gmhmmp_heuristic.pl
  • gms
  • gmsn.pl
  • gmx
  • gmx-completion-gmx.bash
  • gmx-completion.bash
  • GMXRC
  • GMXRC.bash
  • GMXRC.csh
  • GMXRC.zsh
  • GNULICENSE
  • gnuregex.c
  • gnuregex.h
  • gnuregex.o
  • godef
  • goname
  • graphtoprob
  • greedyMatching
  • groupBy
  • gsl-config
  • gsl-histogram
  • gsl-randist
  • gtf2gff.py
  • gtf_juncs
  • gtf_to_fasta
  • gtf_to_sam
  • h5cc
  • h5copy
  • h5debug
  • h5diff
  • h5dump
  • h5import
  • h5jam
  • h5ls
  • h5mkgrp
  • h5perf_serial
  • h5redeploy
  • h5repack
  • h5repart
  • h5stat
  • h5unjam
  • h52gif
  • HaploidifyStatsPlot.pl
  • Happening
  • hash_exp
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  • helixturnhelix
  • HelpMe.pl
  • histogram
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  • HMMERSearchEngine.pm
  • hmmpress
  • hmmscan
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  • hmmsearch
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  • hmm_to_gtf.pl
  • hmoment
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  • htsfile
  • htsfile.org
  • HyperToReftigs
  • idba
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  • ipython
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  • isolasso_pipeline.py
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  • isoseq_classify_report
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  • iupac.c
  • iupac.o
  • jags
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  • jsonschema
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  • julia
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  • juncs_db
  • KAligner
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  • KmerSpectrum
  • KmerSpectrumPlot.pl
  • knowntypes.standard
  • konings.c
  • konings.o
  • konnector
  • KPatch
  • label_ambiguous_fusion_genes.py
  • label_found_fusions.py
  • label_fusion_genes.py
  • last-dotplot
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  • leaff
  • legacy_blast.pl
  • lengthdist.c
  • lengthdist.o
  • lengths_reads.py
  • lib
  • libcanu.a
  • LibCoverage
  • libleaff.a
  • liftover.py
  • lindna
  • linkhsp_unit_test
  • linksBed
  • link_git_modules
  • listor
  • LittleHelpsBig
  • loading_xml
  • LocalizeReadsLG
  • local_map
  • lofreq
  • lofreq2_call_pparallel.py
  • lofreq2_indel_ovlp.py
  • lofreq2_somatic.py
  • lofreq2_vcfplot.py
  • logcounter
  • LongReadConsensus
  • LongReadPostPatcher
  • LongReadsToUnipaths
  • LongReadUnipathPatcher
  • long_seq_tm_test
  • long_spanning_reads
  • lwp-download
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  • lx-ppc64el
  • macs2
  • maf-convert
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  • mafft-distance
  • mafft-homologs.1
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  • Make.sh
  • makeblastdb
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  • Makefile
  • Makefile.am
  • Makefile.in
  • MakeLookupTable
  • makemat
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  • maker
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  • MakeRcDb
  • maker_functional
  • maker_functional_fasta
  • maker_functional_gff
  • maker_map_ids
  • MakeScaffoldsLG
  • makeSCF
  • make_nt_freq_mat.pl
  • make_paramfile
  • mam
  • MANUAL
  • Manual.ps
  • map2assembly
  • map2gtf
  • mapBed
  • mapDamage
  • mapping_stats
  • mapping_stats_poc
  • MapSeeds
  • mapview
  • map_data_ids
  • map_fasta_ids
  • map_gff_ids
  • maq2sam-long
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  • marscan
  • maskambignuc
  • maskambigprot
  • maskFastaFromBed
  • maskfeat
  • maskseq
  • mason.pl
  • maspar.h
  • matcher
  • matinfo
  • maxmodelmaker.c
  • maxmodelmaker.o
  • mccaskillwrap
  • mcl
  • mclcm
  • mclpipeline
  • mcx
  • mcxarray
  • mcxassemble
  • mcxdump
  • mcxi
  • mcxload
  • mcxmap
  • mcxrand
  • mcxsubs
  • md5fa
  • md5sum-lite
  • med2xml
  • megablast
  • megahit
  • megahit_asm_core
  • megahit_sdbg_build
  • megahit_toolkit
  • megamerger
  • MemHogger
  • MemMonitor
  • merge-sam.py
  • mergeBed
  • MergeContigs
  • MergeContigsOnReference
  • MergeNeighborhoods1
  • MergeNeighborhoods2
  • MergeNeighborhoods3
  • MergePairedFastbs
  • MergePaths
  • merger
  • MergeReadSets
  • merge_reports.py
  • meryl
  • mgaps
  • mhap-2.0.jar
  • mhap-2.1.jar
  • mhapConvert
  • miniconda3.sh
  • misc.c
  • misc.o
  • MITObim.pl
  • Mixmer
  • mkmat
  • mmapConvert
  • model.c
  • model.o
  • modelmaking.c
  • modelmaking.o
  • modsclean
  • mothur
  • motifs_report
  • mp-dbviterbi.m
  • mpcovels_main.c
  • mpviterbi.m
  • mrsfast
  • msa2pssm_unit_test
  • msbar
  • msf.c
  • msf.o
  • multi2hat3s
  • multiBamCov
  • multiInd_SetCover
  • multiIntersectBed
  • mummer
  • mummerplot
  • mwcontam
  • mwfilter
  • naifdb-test.pl
  • NaifDB.pm
  • natsort
  • nbib2xml
  • NCBIBlastSearchEngine.pm
  • NCBIBlastXSearchEngine.pm
  • needle
  • needleall
  • newcpgreport
  • newcpgseek
  • newseq
  • NhoodInfo
  • nodes-in-job
  • nohtml
  • noncoding-trainer.pl
  • noreturn
  • nospace
  • notab
  • notseq
  • novel_cluster
  • novo2sam.pl
  • ntdpal
  • nthseq
  • nthseqset
  • ntlookup_unit_test
  • ntscan_unit_test
  • ntthal
  • nucBed
  • nucmer
  • nucmer2xfig
  • octanol
  • oddcomp
  • oea.LocalAssembly
  • OEASetsProb
  • OldPicardCacheToCache.pl
  • oligotm
  • ontocount
  • ontoget
  • ontogetcommon
  • ontogetdown
  • ontogetobsolete
  • ontogetroot
  • ontogetsibs
  • ontogetup
  • ontoisobsolete
  • ontotext
  • opencv_annotation
  • opencv_createsamples
  • opencv_traincascade
  • opencv_visualisation
  • optionshandle_unit_test
  • Overlap
  • overlap.py
  • overlapConvert
  • overlapImport
  • overlapInCore
  • overlapInCorePartition
  • overlapPair
  • overview_report
  • ovStoreBucketizer
  • ovStoreBuild
  • ovStoreDump
  • ovStoreIndexer
  • ovStoreSorter
  • ovStoreStats
  • padding-fastq.py
  • painter.py
  • pair2hat3s
  • pair8removal.py
  • pairash
  • Paired-end_match_sam
  • Paired-end_match_sam.c
  • pairlocalalign
  • pairToBed
  • pairToPair
  • pairToSC.sh
  • pair_match_v5
  • pair_match_v5.c
  • pal2rgb
  • palindrome
  • pandaseq
  • pandaseq-checkid
  • pandaseq-diff
  • pandaseq-hang
  • pandaxs
  • pantherScore.pl
  • parallel-fasta
  • parallel-fastq
  • ParallelSortTest
  • parallel_blat
  • parallel_blat.o
  • parallel_rna_blat
  • parallel_rna_blat.o
  • parasight.pl
  • ParseAligns
  • ParseBlastXmlReport
  • ParseMemMonitorOutput.pl
  • parserQualWReadPrunWSatellite
  • parsewise
  • parse_by_introns.pl
  • parse_ET.pl
  • parse_gibbs.pl
  • parse_set.pl
  • pasteseq
  • pasteurize
  • patch-hmm.pl
  • PatcherCottage
  • PathConsensus
  • PathOverlap
  • PathReads
  • PathsToLocs
  • patmatdb
  • patmatmotifs
  • pavesi.c
  • pavesi.o
  • pbservice
  • pbvalidate
  • pear
  • pepcoil
  • pepdigest
  • pepinfo
  • pepnet
  • pepstats
  • pepwheel
  • pepwindow
  • pepwindowall
  • PerlRunTime.pm
  • PerlUtils.pm
  • pfscan
  • pfsearch
  • pfsearch_wrapper.py
  • phiblast_unit_test
  • phred.py
  • PicardToCache.pl
  • PickTheRightBranch
  • pilconvert.py
  • pildriver.py
  • pilfile.py
  • pilfont.py
  • pilprint.py
  • pip
  • pip2
  • pip2.7
  • pirsf.pl
  • PIRSF.pm
  • plankton
  • play
  • player.py
  • plot-bamstats
  • plotcon
  • plotorf
  • plotter.py
  • plurality
  • pmath
  • polydot
  • PopBubbles
  • postnuc
  • PostPatcher
  • PostPatcherBuildJoins
  • postpro
  • ppm2tiff
  • preassembly_report
  • predict_frame.py
  • predict_genes.pl
  • predict_graphs.py
  • predict_splicegraph.py
  • prefixEditDistance-matchLimitGenerate
  • preg
  • prelimsearch_unit_test
  • prenuc
  • prepareAlign
  • PrepareAllPathsInputs.pl
  • PrepareGenome
  • prepro
  • preprocPair_with_inlineBC.py
  • prep_reads
  • prerapsearch
  • prettyplot
  • prettyseq
  • primer3_core
  • primersearch
  • printsextract
  • print_graph
  • print_graph.o
  • prior.c
  • prior.h
  • prior.o
  • probify.c
  • probify.o
  • probuild
  • process-scheduler-log
  • ProcessRepeats
  • prodigal
  • ProDomBlast3i.pl
  • profit
  • progress.R
  • project_tree_builder
  • promer
  • prophecy
  • prophet
  • prosextract
  • prove
  • PRSearchResult.pm
  • pscan
  • PSELC.cm
  • PSELCinf-c.cm
  • psginfer_pipeline.py
  • psginfer_update_graphs.py
  • psibl2seq_unit_test
  • psiblast
  • psiblast_iteration_unit_test
  • psiblast_unit_test
  • psiphi
  • psl2sam.pl
  • psl_best_unique_contigs.py
  • pssmcreate_unit_test
  • pssmenginefreqratios_unit_test
  • ps_gm_overlay.pl
  • ps_scan.pl
  • pt2to3
  • ptdump
  • ptrepack
  • pttree
  • PubRef.pm
  • PunchTandemHoles
  • puudecode
  • puuencode
  • pydoc
  • pynast
  • pyqi
  • python
  • python-config
  • python2
  • python2-config
  • python2.7
  • python2.7-config
  • python_version.py
  • qacct
  • qalter
  • qcli_make_rst
  • qcli_make_script
  • qconf
  • qdel
  • qevent
  • qhold
  • qhost
  • qlogin
  • qmod
  • qping
  • qquota
  • qrdel
  • qresub
  • qrls
  • qrsh
  • qrstat
  • qrsub
  • qsched
  • qselect
  • qselect-node-list
  • qsh
  • qstat
  • qstatus
  • qsub
  • Quala2Qualb
  • Qualb2Quala
  • QualbStats
  • QualbStatsPlot.pl
  • QualsStatsAddToCache.pl
  • querydata_unit_test
  • queryinfo_unit_test
  • QueryLookupTable
  • quiver
  • rake
  • randomBed
  • rand_graph
  • rapsearch
  • ras2tiff
  • raw2tiff
  • raw_n50
  • raw_n50.o
  • rdoc
  • readConsensus
  • ReadFilterByKmerFreq
  • readlink.sh
  • README
  • reads_from_map.py
  • ReadTrack
  • realignment_pipeline.py
  • rebaseextract
  • RebuildAssemblyFiles
  • rec
  • recoder
  • RecoverPunchTandem
  • RecoverUnipaths
  • redata
  • redoalignment_unit_test
  • reduce_amplicons.R
  • reformat_fasta.pl
  • reformat_gff.pl
  • reformat_main.c
  • refseqget
  • regtable2seq
  • Release.history
  • remap
  • RemodelGaps
  • remote_blast_unit_test
  • remove-adapter.py
  • remove-bad-illumina.py
  • RemoveDodgyReads
  • RemoveHighCNAligns
  • remove_custom_feature.py
  • remove_reads_exon_exon_fastq.py
  • remove_reads_exon_exon_map.py
  • remove_reads_exon_exon_psl.py
  • remove_reads_genome_transcriptome.py
  • remove_shorter_reads.py
  • remove_str.py
  • RepbaseEMBL.pm
  • RepbaseRecord.pm
  • repeat-match
  • RepeatMasker
  • RepeatMaskerConfig.tmpl
  • RepeatProteinMask
  • ReplacePairsStats
  • replaceu
  • rescale_gff.pl
  • restoreu
  • restover
  • restrict
  • retrieve_seq_from_fasta.pl
  • revcomp.c
  • revcomp.o
  • revcomp_main.c
  • revseq
  • rgb2ycbcr
  • ri
  • ris2xml
  • rkhunter
  • rmblastn
  • rnaseq_introns_to_gff.pl
  • rnatest
  • rpsblast
  • rpstblastn
  • rps_unit_test
  • rsem-bam2readdepth
  • rsem-bam2wig
  • rsem-build-read-index
  • rsem-calculate-credibility-intervals
  • rsem-extract-reference-transcripts
  • rsem-get-unique
  • rsem-parse-alignments
  • rsem-preref
  • rsem-run-em
  • rsem-run-gibbs
  • rsem-sam-validator
  • rsem-scan-for-paired-end-reads
  • rsem-simulate-reads
  • rsem-synthesis-reference-transcripts
  • rsem-tbam2gbam
  • ruby
  • run-mummer1
  • run-mummer3
  • RunAllPathsLG
  • runJemboss.sh
  • run_hmm_pbs.pl
  • run_microbe_census.py
  • sam2psl.py
  • sam2vcf.pl
  • SamplePairedReadDistributions
  • SamplePairedReadStats
  • sample_reads
  • sample_reads.o
  • samtools
  • samtools.pl
  • samtools_0.1.18
  • sam_collate.py
  • sam_filter.py
  • sam_juncs
  • sam_split.py
  • sam_to_depths.py
  • save.c
  • save.o
  • scaffold
  • scaffold.o
  • ScaffoldAccuracy
  • ScaffoldGraphToGnuplot
  • ScaffoldLayout
  • scan_for_bp.pl
  • scan_main.c
  • scan_main.o
  • scf_dump
  • scf_info
  • scf_update
  • score
  • scoreblk_unit_test
  • scorestack.c
  • scorestack.o
  • score_main.c
  • score_main.o
  • scramble
  • scram_flagstat
  • scram_merge
  • scram_pileup
  • scram_test
  • SearchEngineI.pm
  • SearchResult.pm
  • SearchResultCollection.pm
  • search_strategy_unit_test
  • seealso
  • seedtop
  • segmasker
  • segment_juncs
  • SelectRandomPairs
  • SelectSeeds
  • select_model_parameters.py
  • selex.c
  • selex.o
  • seq2regtable
  • seqcount
  • SeqDBI.pm
  • seqdb_demo
  • seqdb_perf
  • seqdb_unit_test
  • SeqInfo
  • seqinfosrc_unit_test
  • seqmatchall
  • seqret
  • seqretsetall
  • seqretsplit
  • seqsrc_unit_test
  • seqstat_main.c
  • seqtk-subseq.sh
  • seqxref
  • seqxrefget
  • seq_cache_populate.pl
  • servertell
  • setcore
  • setCoverProbWeighted
  • setdirection
  • setup.tRNAscan-SE
  • setupfactory_unit_test
  • sextet5
  • sge-disable-submits
  • sge-enable-submits
  • sgepasswd
  • sge_coshepherd
  • sge_execd
  • sge_qmaster
  • sge_shadowd
  • sge_share_mon
  • sge_shepherd
  • ShaveUnipathGraph
  • shield_genes.py
  • shiftBed
  • ShortQueryLookup
  • show-aligns
  • show-coords
  • show-diff
  • show-snps
  • show-tiling
  • showalign
  • showdb
  • showfeat
  • showorf
  • showpep
  • showseq
  • showserver
  • shuffle.py
  • shuffleBed
  • shuffleseq
  • shuffle_main.c
  • shuffle_reads
  • shuffle_reads.o
  • sigcleave
  • silent
  • simple
  • SimpleBatcher.pm
  • SimpleGapCloser
  • SimpleGraph
  • sim_reads
  • sim_reads.o
  • sim_reads_tran
  • sim_reads_tran.o
  • Sipros_OpenMP
  • sirna
  • sixpack
  • sizeseq
  • skipredundant
  • skipseq
  • skivi
  • slopBed
  • smallviterbi.c
  • smallviterbi.o
  • smi
  • smoothing_fusions_psl.py
  • smtpd.py
  • snap
  • soap2sam.pl
  • SOAPdenovo-31mer
  • SOAPdenovo-63mer
  • SOAPdenovo-127mer
  • SOAPsh.pl
  • solexa18to15.py
  • sortBed
  • sortedcontainers
  • sortString
  • sort_psl
  • sort_psl.o
  • sort_reads
  • sort_reads.o
  • sort_ttdb.py
  • sox
  • soxi
  • splicegraph_statistics.py
  • splice_junction_pipeline.py
  • split-fasta.py
  • split-reads.py
  • SplitOEA_match
  • SplitOEA_match.c
  • SplitReadAll_lite
  • SplitReadAll_lite.c
  • splitReads
  • splitReadsBySample.py
  • splitsource
  • splittbfast
  • splitter
  • SplitUnibases
  • split_fa
  • split_fa.o
  • split_fq
  • split_fq.o
  • split_match_sam
  • split_match_sam.c
  • split_query_unit_test
  • split_scaffold
  • split_scaffold.o
  • sqerror.c
  • sqerror.o
  • sqfuncs.h
  • sqio.c
  • sqio.o
  • sqlite3
  • squid.h
  • sra2illumina.py
  • sra_to_solid
  • sre_ctype.c
  • sre_ctype.o
  • sre_math.c
  • sre_math.o
  • sre_string.c
  • sre_string.o
  • srf2fasta
  • srf2fastq
  • srf_dump_all
  • srf_extract_hash
  • srf_extract_linear
  • srf_filter
  • srf_index_hash
  • srf_info
  • srf_list
  • srf_split_by_tag
  • sstofa
  • sstofa.pl
  • stack.c
  • stack.o
  • stag-autoschema.pl
  • stag-db.pl
  • stag-diff.pl
  • stag-drawtree.pl
  • stag-filter.pl
  • stag-findsubtree.pl
  • stag-flatten.pl
  • stag-grep.pl
  • stag-handle.pl
  • stag-itext2simple.pl
  • stag-itext2sxpr.pl
  • stag-itext2xml.pl
  • stag-join.pl
  • stag-merge.pl
  • stag-mogrify.pl
  • stag-parse.pl
  • stag-query.pl
  • stag-splitter.pl
  • stag-view.pl
  • stag-xml2itext.pl
  • star_to_gff.pl
  • stat.pl
  • stretcher
  • stringtie
  • structcheck_main.c
  • structs.c
  • structs.h
  • structs.o
  • stssearch
  • stubmaker.pl
  • subj_ranges_unit_test
  • SubmissionPrep
  • subtractBed
  • summarizeConsensus
  • summarize_compare_by_movie
  • summarize_coverage
  • sumtrees.py
  • sumtrees.pyc
  • superfamily.pl
  • supermatcher
  • syco
  • symbols.py
  • tabix
  • tabix.org
  • table_annovar.pl
  • tagBam
  • TagCircularScaffolds
  • taxget
  • taxgetdown
  • taxgetrank
  • taxgetspecies
  • taxgetup
  • Taxonomy.pm
  • tbfast
  • tblastn
  • tblastx
  • tcode
  • test
  • test-yaml
  • test.o
  • testrun.ref
  • textget
  • textsearch
  • tfextract
  • tfm
  • tfscan
  • tgStoreCompress
  • tgStoreCoverageStat
  • tgStoreDump
  • tgStoreFilter
  • tgStoreLoad
  • tgTigDisplay
  • theano-cache
  • theano-nose
  • theta
  • thresholder.py
  • thumbnail
  • tiff2bw
  • tiff2pdf
  • tiff2ps
  • tiff2rgba
  • tiffcmp
  • tiffcp
  • tiffcrop
  • tiffdither
  • tiffdump
  • tiffgt
  • tiffinfo
  • tiffmedian
  • tiffset
  • tiffsplit
  • tmap
  • tophat
  • tophat-fusion-post
  • tophat2
  • tophat2gff3
  • tophat_reports
  • TPCsignal
  • trace.c
  • trace.o
  • tracebacksearch_unit_test
  • traceback_unit_test
  • trace_dump
  • train_main.c
  • tranalign
  • transeq
  • TRF.pm
  • TRFResult.pm
  • TRFSearchResult.pm
  • trimest
  • trimmomatic.jar
  • trimReads
  • trimseq
  • trimspace
  • trim_poly_tails.py
  • trim_reads.py
  • Trinity
  • TRNA2-arch.cm
  • TRNA2-archns.cm
  • TRNA2-bact.cm
  • TRNA2-bactns.cm
  • TRNA2-euk.cm
  • TRNA2-eukns.cm
  • TRNA2.cm
  • TRNA2ns.cm
  • TRNAinf-arch-3h-nc.cm
  • TRNAinf-arch-5h-nc.cm
  • TRNAinf-arch-c.cm
  • TRNAinf-arch-ns-c.cm
  • TRNAinf-bact-c.cm
  • TRNAinf-bact-ns-c.cm
  • TRNAinf-c.cm
  • TRNAinf-euk-c.cm
  • TRNAinf-euk-ns-c.cm
  • TRNAinf-ns-c.cm
  • trnascan-1.4
  • tRNAscan-SE
  • tRNAscan-SE-original
  • tRNAscan-SE.man
  • tRNAscan-SE.src
  • trnascan.c
  • trnascan.o
  • TrueUnipathCoverage
  • twofeat
  • type1to2convertor
  • types.c
  • types.o
  • uchime
  • UnibaseCopyNumber3
  • uniform_search_unit_test
  • union
  • unionBedGraphs
  • UnipathBabyStats
  • Unipather
  • UnipatherBig
  • UnipathEval
  • UnipathLocsLG
  • UnipathPatcher
  • unique
  • UniquifyAligns2
  • unzip
  • unzipsfx
  • update_blastdb.pl
  • update_git_modules
  • update_velvet.sh
  • urlget
  • use-devel-checklib
  • utgcns
  • ValidateAllPathsInputs
  • validate_component
  • validate_component.o
  • validate_contigs_blat
  • validate_contigs_blat.o
  • validate_contigs_mummer
  • validate_contigs_mummer.o
  • validate_reads_blat
  • validate_reads_blat.o
  • validate_rna
  • validate_rna.o
  • varfilter.py
  • variantCaller
  • variants_reduction.pl
  • variationget
  • VariationHunter_SC
  • vcf-annotate
  • vcf-compare
  • vcf-concat
  • vcf-consensus
  • vcf-contrast
  • vcf-convert
  • vcf-fix-newlines
  • vcf-fix-ploidy
  • vcf-indel-stats
  • vcf-isec
  • vcf-merge
  • vcf-phased-join
  • vcf-query
  • vcf-shuffle-cols
  • vcf-sort
  • vcf-stats
  • vcf-subset
  • vcf-to-tab
  • vcf-tstv
  • vcf-validator
  • vcftools
  • vectorstrip
  • velvetg
  • velveth
  • verify_evidence_gmhmm.pl
  • version
  • version.h
  • version_reference_unit_test
  • VH
  • viewer.py
  • viewmat
  • view_splicegraphs.py
  • view_splicegraph_multiplot.py
  • virtualenv
  • viterbi.c
  • viterbi.o
  • vsearch
  • water
  • wgsim
  • wgsim_eval.pl
  • wheel
  • whichdb
  • windowBed
  • windowMaker
  • windowmasker
  • windowmasker_2.2.22_adapter.py
  • wobble
  • wordbib2xml
  • wordcount
  • wordfinder
  • wordmatch
  • workflow.py
  • wossdata
  • wossinput
  • wossname
  • wossoperation
  • wossoutput
  • wossparam
  • wosstopic
  • writedb_unit_test
  • WUBlastSearchEngine.pm
  • WUBlastXSearchEngine.pm
  • xml2ads
  • xml2bib
  • xml2end
  • xml2isi
  • xml2ris
  • xml2wordbib
  • xplor2gmx.pl
  • yank
  • zff2gff3.pl
  • zipdetails
  • zipgrep
  • zipinfo
  • zoom2sam.pl
  • ztr_dump