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Title:	Artemis Software List
Owner:	Stephen Kolmann
Creator:	Stephen Kolmann	Dec 06, 2017
Last Changed by:	Stephen Kolmann	Aug 19, 2019
Tiny Link: (useful for email)	https://sydneyuni.atlassian.net/wiki/x/AQAEEQ
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Outgoing Links

External Links (1097)

https://ccb.jhu.edu/software/bracken/index.shtml?t=manual

www.atgc-montpellier.fr/LSD/

https://github.com/EVidenceModeler/EVidenceModeler/releases

mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.h…

https://golang.org/

https://developers.google.com/protocol-buffers/

https://github.com/voutcn/megahit

www.drive5.com/

www.unidata.ucar.edu/software/udunits/#documentation

julialang.org/

huttenhower.sph.harvard.edu/metaphlan2

csb5.github.io/lofreq/commands/

https://github.com/COMBINE-lab/salmon

bioinfo.lifl.fr/RNA/sortmerna/code/SortMeRNA-user-manual-v1…

https://samtools.github.io/bcftools/bcftools.html

https://github.com/google/re2/wiki

https://github.com/jbeder/yaml-cpp

cortexassembler.sourceforge.net/cortex_var_user_manual.pdf

https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/sh…

https://www.gnu.org/software/bison/

eddylab.org/software/hmmer3/3.1b2/Userguide.pdf

valgrind.org/

www.slimsuite.unsw.edu.au/software.php

https://www.bioinformatics.babraham.ac.uk/projects/hicup/re…

t-ogasawara.github.io/sam-to-bam/

https://cmake.org/

www.opengatecollaboration.org/

www.openblas.net/

https://github.com/google/re2

denovoassembler.sourceforge.net/manual.html

https://github.com/rordenlab/dcm2niix

www.bonvinlab.org/software/haddock2.2/manual/

https://ccb.jhu.edu/software/FLASH/

https://pandoc.org/

dti-tk.sourceforge.net/pmwiki/pmwiki.php

https://github.com/baoe/AlignGraph

fismed.ciemat.es/GAMOS/

https://github.com/lh3/minimap2#users-guide

https://gflags.github.io/gflags/

https://github.com/tijeco/FUSTr

https://matlabacademy.mathworks.com/

https://computation.llnl.gov/sites/default/files/public/hyp…

www.mykrobe.com/products/predictor/

www.unidata.ucar.edu/software/udunits/

busco.ezlab.org/

https://elpa.mpcdf.mpg.de/documentation

www.personal.psu.edu/mxd60/sf2.html

https://pachterlab.github.io/kallisto/download

iubio.bio.indiana.edu/soft/molbio/readseq/java/

libjpeg.sourceforge.net/

https://www.ruby-lang.org/en/documentation/

mcmc-jags.sourceforge.net/

https://github.com/cole-trapnell-lab/cufflinks

glaros.dtc.umn.edu/gkhome/metis/metis/overview

https://cgns.github.io/

yasm.tortall.net/

https://git-scm.com/

catchenlab.life.illinois.edu/stacks/manual/

metavelvet.dna.bio.keio.ac.jp/

stnava.github.io/ANTs/

https://rc.sydney.edu.au/matlab-gateway/

gmsh.info/

https://sites.google.com/site/hipposubfields/home

sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=km…

yasm.tortall.net/Guide.html

docs.aws.amazon.com/cli/latest/userguide/installing.html

https://github.com/gperftools/gperftools/wiki

invisible-island.net/mawk/mawk.html#documentation

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL

cnsgenomics.com/software/gcta/download.html

gts.sourceforge.net/

abacus.gene.ucl.ac.uk/ziheng/pdf/2015YangCZv61p854.pdf

https://sydneyuni.atlassian.net/wiki/spaces/RC/pages/229114…

canu.readthedocs.io/en/latest/

https://atgu.mgh.harvard.edu/xhmm/index.shtml

https://support.10xgenomics.com/single-cell-gene-expression…

ant.apache.org/

https://github.com/tseemann/shovill

denovoassembler.sourceforge.net/

genetics.cs.ucla.edu/emmax/

https://github.com/GregoryFaust/samblaster

eddylab.org/infernal/Userguide.pdf

https://github.com/gt1/libmaus2

https://github.com/PacificBiosciences/blasr/wiki

https://www.ode.org/

https://github.com/GNOME/libcroco/tree/master/docs

https://sourceforge.net/projects/netgen-mesher/

bioinf.spbau.ru/spades

https://www.tensorflow.org/community/documentation

https://sourceforge.net/projects/openfoamplus/files/v1612%2…

https://github.com/jts/nanopolish

smithlabresearch.org/software/methpipe/

https://www.freetype.org/freetype2/docs/documentation.html

camino.cs.ucl.ac.uk/

pslib.sourceforge.net/

https://support.hdfgroup.org/HDF5/doc/UG/HDF5_Users_Guide-R…

https://www.gnu.org/software/emacs/

https://www.cs.umd.edu/~mount/ANN/Files/1.1.2/ANNmanual_1.1…

https://www.nitrc.org/projects/conn/

www.fftw.org/#documentation

https://github.com/statgen/fastQValidator

geant4.web.cern.ch/geant4/support/gettingstarted.shtml

https://github.com/maasha/biopieces

beast.bio.ed.ac.uk/home#toc-4

https://www.nasm.us/

https://www.otago.ac.nz/cs/groups/public/@biochemistry/docu…

rapidjson.org/index.html

https://github.com/isovic/racon

mxnet.io/

https://github.com/tseemann/abricate

https://github.com/pezmaster31/bamtools/wiki

www.atgc-montpellier.fr/fastme/usersguide.php

https://pugixml.org/

https://www.gnu.org/software/ncurses/

https://expressionanalysis.github.io/ea-utils/

torch.ch/

https://github.com/google/glog

popgen.sc.fsu.edu/Migrate/Migrate-n.html

snpeff.sourceforge.net/SnpEff_manual.html

www.nature.com/nature/journal/v449/n7164/full/nature06250.h…

www.people.fas.harvard.edu/~junliu/Haplo/click.html

hartleys.github.io/QoRTs/index.html

https://elpa.mpcdf.mpg.de/

https://github.com/theaidenlab/juicer/blob/master/README.md

ab-initio.mit.edu/wiki/index.php/NLopt_manual

https://github.com/underworldcode/underworld2

https://gforge.inria.fr/docman/view.php/248/8261/ptscotch_u…

www.megasoftware.net/web_help_7/helpfile.htm#hc_first_time_…

stxxl.org/tags/master/

www.megasoftware.net/

https://omictools.com/juicer-tool

https://github.com/marbl/Mash

cbg-ethz.github.io/shorah/

https://github.com/HpcGridRunner/HpcGridRunner

www.cbs.dtu.dk/services/SignalP/

project-osrm.org/docs/v5.6.0/api/#general-options

https://cmake.org/documentation/

https://github.com/OpenGene/fastp

https://www.vapor.ucar.edu/docs/usage

https://github.com/yulequan/3D-Caffe

www.stjuderesearch.org/site/lab/zhang

astro.dur.ac.uk/~jch/gadgetviewer/index.html

https://tcl.tk/doc/

https://github.com/dpryan79/methyldackel

https://gephi.org/users/

https://www.scala-lang.org/

brewformulas.org/s-lang

www.well.ox.ac.uk/platypus-doc

arma.sourceforge.net/docs.html

www.graphviz.org/

https://www.gnu.org/software/libtool/manual/

https://orcaforum.kofo.mpg.de/

bioinfo.ut.ee/download/dl.php?file=12

www.harrisgeospatial.com/ProductsandSolutions/GeospatialPro…

csg.sph.umich.edu/abecasis/mach/

https://github.com/tseemann/samclip

www.molpro.net/info/2015.1/doc/manual/index.html?portal=use…

www.repeatmasker.org/

https://www.inf.ethz.ch/personal/fukudak/cdd_home/

dicom.offis.de/dcmtk.php.en

https://github.com/tseemann/snippy

https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/

https://cran.r-project.org/web/packages/rgdal/rgdal.pdf

https://sylabs.io/singularity/

https://www.open-mpi.org/doc/

www.yandell-lab.org/software/maker.html

https://sourceware.org/libffi/

https://tiswww.case.edu/php/chet/readline/rltop.html

https://nim-lang.org/documentation.html

https://fbb-git.github.io/icmake/

www.vicbioinformatics.com/documents/Quick_Start_Guide_BLAST…

ghmm.sourceforge.net/documentation.html

www.vicbioinformatics.com/software.prokka.shtml

popgen.sc.fsu.edu/Migrate/Tutorials/Tutorials.html

weizhongli-lab.org/lab-wiki/doku.php?id=cd-hit-user-guide

www.atnf.csiro.au/people/mcalabre/WCS/

https://github.com/bonsai-team/matam

https://www.gnu.org/software/gsl/manual/html_node/

www.drive5.com/usearch/manual/

https://www.sourceware.org/gdb/

https://www.lua.org/docs.html

gmsh.info/doc/texinfo/gmsh.html

www.drive5.com/usearch/

https://gcc.gnu.org/onlinedocs/

trimal.cgenomics.org/

https://www.gnu.org/software/libunistring/

https://www.paraview.org/resources/

cortexassembler.sourceforge.net/

sco.h-its.org/exelixis/resource/download/NewManual.pdf

www.swig.org/

https://github.com/TGAC/KAT

microbiomeutil.sourceforge.net/

gnudatalanguage.sourceforge.net/

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/H…

plplot.sourceforge.net/documentation.php

https://tiswww.case.edu/php/chet/readline/rltop.html#Docume…

www.graphicsmagick.org/

www.gdal.org/

zeromq.org/

geant4.web.cern.ch/geant4/

valgrind.org/docs/manual/index.html

https://www.ncbi.nlm.nih.gov/books/NBK279671/

gitlab.com/ezlab/busco/raw/master/BUSCO_v3_userguide.pdf

last.cbrc.jp/

https://biosails.github.io/pheniqs/

https://www.systutorials.com/docs/linux/man/1-gengetopt/

www.well.ox.ac.uk/platypus

https://github.com/mjsull/HapFlow/wiki

https://github.com/behdad/harfbuzz/wiki

https://github.com/alexdobin/STAR

https://aria2.github.io/

biogeme.epfl.ch/pdfdocuments.html

bowtie-bio.sourceforge.net/manual.shtml

www.bioinformatics.babraham.ac.uk/projects/fastqc/

www.pango.org/

gpi.unibe.ch/

https://poppler.freedesktop.org/

https://www.imagemagick.org/discourse-server/viewtopic.php?…

https://developer.gnome.org/glib/

https://libspatialindex.github.io/

www.faqs.org/faqs/jpeg-faq/

https://root.cern.ch/documentation

https://www.gnu.org/software/binutils/

exon.gatech.edu/GeneMark/

https://bix.ucsd.edu/repeatscout/readme.1.0.5.txt

https://github.com/kingsfordgroup/armatus/blob/master/READM…

www.quantum-espresso.org/users-manual/

catchenlab.life.illinois.edu/stacks/

www.rasterbar.com/products/luabind/docs.html

www.pacb.com

https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual

freeglut.sourceforge.net/

https://www.wolfram.com/mathematica/

https://github.com/alastair-droop/fqtools

https://www.imagemagick.org/script/index.php

https://libgd.github.io/

www.vmatch.de/virtman.pdf

melt.igs.umaryland.edu/manual.php

www.openrtk.org/

https://github.com/FelixKrueger/Bismark/tree/master/Docs

phobius.sbc.su.se/

torch.ch/docs/getting-started.html#_

circos.ca/documentation/

https://golang.org/doc/

https://www.ncbi.nlm.nih.gov/toolkit

www.quantum-espresso.org/

facebook.github.io/zstd/zstd_manual.html

https://github.com/gt1/biobambam2

https://github.com/westes/flex/tree/master/doc

mrbayes.sourceforge.net/

www.genomekorea.com/display/tools/HLAscan

www.clustal.org/omega/

https://github.com/abyzovlab/CNVnator

https://curl.haxx.se/

www.boost.org/

circos.ca/software/

https://bitbucket.org/berkeleylab/metabat/src/master/

lipid.biocuckoo.org/

https://github.com/gemtools/gemtools

www.mlst.net/

https://github.com/gt1/bambamc

https://www.gnu.org/software/libtool/libtool.html

https://github.com/neufeld/pandaseq

https://github.com/hyattpd/prodigal/wiki

slepc.upv.es/

www.multiprecision.org/mpc/documentation.html

https://lbgi.fr/AnnotSV/

genetics.cs.ucla.edu/emmax/install.html

argtable.sourceforge.net/

https://maven.apache.org/

https://github.com/yade

https://cran.r-project.org/manuals.html

https://developers.google.com/protocol-buffers/docs/overvie…

https://ghostscript.com/doc/9.15/Readme.htm

gatkforums.broadinstitute.org/gatk/categories/mutect-docume…

https://bitbucket.org/biobakery/biobakery/wiki/metaphlan2

https://trinotate.github.io/

https://libspectre.freedesktop.org/manual/

www.lstc.com/download/manuals

ftp://ftp.dl.ac.uk/ccp5/DL_POLY/DL_POLY_4.0/DOCUMENTS/USRMA…

www.htslib.org/doc/#manual-pages

www.netlib.org/lapack/

https://sourceforge.net/projects/mathgl/files/mathgl/mathgl…

ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/Al…

meme-suite.org/doc/overview.html?man_type=web

www.well.ox.ac.uk/project-stampy

www.broadinstitute.org/software/igv/igvtools_commandline

https://github.com/ctSkennerton/minced

fulcrumgenomics.github.io/fgbio/

darlinglab.org/mauve/user-guide/introduction.html

https://bioinf.shenwei.me/seqkit/

https://www.nasm.us/docs.php

homepages.math.uic.edu/~jan/PHCpack/phcpack.html

stephenslab.uchicago.edu/software.html#hotspotter

https://sydneyuni.atlassian.net/wiki/spaces/RC/pages/733085…

docs.aws.amazon.com/cli/latest/userguide/cli-chap-welcome.h…

https://sourceforge.net/projects/franzpedigree/files/

www.libpng.org/pub/mng/mngdocs.html

https://subversion.apache.org/docs/

https://sourceforge.net/p/codonphyml/wiki/Home/

https://imagej.nih.gov/ij/

www.vtk.org/vtk-users-guide/

meteora.ucsd.edu/~pierce/ncview_home_page.html

genometools.org/documentation.html

https://sourceforge.net/p/artfastqgen/wiki/Home/

https://www.ece.uvic.ca/~frodo/jasper/

https://docs.npmjs.com/

www.lstc.com/lspp/

https://www.rosettacommons.org/docs/latest/Home

www.sanger.ac.uk/science/tools/smalt-0

https://github.com/tseemann/snp-dists

www.ks.uiuc.edu/Research/namd/

https://github.com/abyzovlab/vcf2diploid

omics.informatics.indiana.edu/FragGeneScan/

https://www.gnu.org/software/automake/

eddylab.org/software/tRNAscan-SE/

https://www.libsdl.org/projects/SDL_image/

ab-initio.mit.edu/wiki/index.php/Nlopt

https://curl.haxx.se/libcurl/c/libcurl-tutorial.html

deweylab.biostat.wisc.edu/detonate/

www.cmpg.unibe.ch/software/PGDSpider/

math-atlas.sourceforge.net/

https://vcftools.github.io/examples.html

https://directory.fsf.org/wiki/Libelf

https://www.mono-project.com/docs/

deweylab.github.io/RSEM/

https://www.anaconda.com/

freeimage.sourceforge.net/fip/index.html

https://github.com/lh3/seqtk

bowtie-bio.sourceforge.net/bowtie2/index.shtml

www.netlib.org/blas/#_documentation

www.unidata.ucar.edu/software/netcdf/docs/user_guide.html

https://nanoporetech.com/resource-centre/publications/nanoo…

www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Tri…

https://docs.bazel.build/

melt.igs.umaryland.edu/

gaussian.com/

seq.cs.iastate.edu/cap3.html

chiulab.ucsf.edu/surpi/

www.htslib.org/doc/tabix.html

https://www.paraview.org/

https://support.illumina.com/sequencing/sequencing_software…

freeglut.sourceforge.net/docs/api.php

www.plumed.org/

evolution.genetics.washington.edu/phylip/phylip.html

https://www.sqlite.org/

https://github.com/PacificBiosciences/FALCON/wiki

www.bzip.org/

www.gurobi.com/

manual.gromacs.org/documentation/

animalbiosciences.uoguelph.ca/~msargol/fimpute/

www.xzlab.org/software.html

https://www.openssl.org/docs/

https://github.com/tseemann/barrnap

lbbe.univ-lyon1.fr/SiLiX?lang=en

https://biosails.github.io/pheniqs/manual.html

https://www.gnu.org/software/autoconf/autoconf.html

https://www.freedesktop.org/wiki/Software/libspectre/

www.rannala.org/inference-of-recent-migration/

www.qhull.org/

varscan.sourceforge.net/using-varscan.html

mathgen.stats.ox.ac.uk/impute/impute_v2.html

mbio-serv2.mbioekol.lu.se/ARAGORN/

sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=km…

www.zlib.net/

https://www.freedesktop.org/software/fontconfig/fontconfig-…

https://github.com/nextgenusfs/funannotate

https://www.gnu.org/software/libmatheval/

https://developer.gnome.org/pango/unstable/

proj-clhep.web.cern.ch/proj-clhep/index.html#docu

gaussian.com/man/

https://integrativemodeling.org/libTAU.html

https://www.gaia-gis.it/fossil/readosm/index

fastml.tau.ac.il/

https://github.com/ncbi/sratoolkit

https://ccb.jhu.edu/software/kraken/

https://www.freedesktop.org/wiki/Software/dbus/#index4h1

https://www.mongodb.com/

https://www.pymol.org/

https://www.python.org/doc/

www.ccb.jhu.edu/software/centrifuge/manual.shtml

https://genome.ucsc.edu/goldenPath/help/blatSpec.html

fismed.ciemat.es/GAMOS/gamos_userguide.php

https://curl.haxx.se/docs/

bio-bwa.sourceforge.net/

abacus.gene.ucl.ac.uk/software/paml.html

meteora.ucsd.edu/~pierce/docs/ncview.README

liulab.dfci.harvard.edu/MACS/README.html

www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate-…

www.swig.org/Doc1.1/HTML/Contents.html

eddylab.org/infernal/

https://zlib.net/pigz/

genetics.cs.ucla.edu/metatissue/faq.html

openil.sourceforge.net/

https://tcl.tk/

cutadapt.readthedocs.io/en/stable/index.html

www.ks.uiuc.edu/Training/Tutorials/#namd

https://mipav.cit.nih.gov/

spades.bioinf.spbau.ru/release3.10.1/manual.html

https://www.rstudio.com/

www.ccb.jhu.edu/software/centrifuge

https://genome.ucsc.edu/FAQ/FAQblat.html

https://www.gnu.org/software/bison/manual/

https://github.com/scapella/trimal

gaussian.com/citation/

https://www.gaia-gis.it/fossil/virtualpg/wiki?name=tutorial

scons.org/

https://github.com/tseemann/quicktree

https://developer.nvidia.com/cuda-toolkit-20-august-2008

https://sourceforge.net/projects/mathgl/

https://www.cfdem.com/media/DEM/docu/Manual.html

https://genome.sph.umich.edu/wiki/FastQValidator

bowtie-bio.sourceforge.net/index.shtml

beast.bio.ed.ac.uk/

https://github.com/CPTR-ReSeqTB/UVP

rnaseq-mats.sourceforge.net/rmats3.0.9/

cegg.unige.ch/pub/nwutils_tutorial-1.6.pdf

lipid.biocuckoo.org/userguide.php

eigen.tuxfamily.org/index.php?title=Main_Page#Documentation

biogeme.epfl.ch/home.html

www.netlib.org/scalapack/

https://sanger-pathogens.github.io/Roary/

www.pixman.org/

https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/sh…

ab.inf.uni-tuebingen.de/data/software/megan6/download/welco…

bioinf.spbau.ru/sibelia

https://www.gnu.org/software/octave/doc/interpreter/

https://support.hdfgroup.org/HDF5/

www.cgal.org/documentation.html

snap.cs.berkeley.edu/

https://github.com/hahnlab/CAFExp

www.people.fas.harvard.edu/~junliu/Haplo/docMain.htm

abacus.gene.ucl.ac.uk/software/pamlDOC.pdf

https://broadinstitute.github.io/picard/

https://www.gnu.org/software/automake/#documentation

www.mpfr.org/mpfr-current/#doc

https://github.com/torognes/vsearch/wiki

faculty.cse.tamu.edu/davis/suitesparse.html

https://www.sanger.ac.uk/science/tools/artemis

https://openslide.org/

https://github.com/ivmai/bdwgc

https://bedops.readthedocs.io/en/latest/

https://code.google.com/archive/p/batmeth/wikis

https://bitbucket.org/kosaidtu/norgal

https://www.gnu.org/software/octave/

https://github.com/uclouvain/openjpeg/wiki/Installation

https://github.com/fenderglass/Ragout

https://support.aarnet.edu.au/hc/en-us/articles/11500716850…

mxnet.io/tutorials/index.html

https://bix.ucsd.edu/repeatscout/

www.well.ox.ac.uk/~gerton/README.txt

www.libtiff.org/

ftp://ftp.sanger.ac.uk/pub/project/pathogens/gubbins/Gubbin…

https://mothur.org/wiki/Main_Page

https://support.10xgenomics.com/de-novo-assembly/software/o…

simplecryoem.com/manuals.html

https://github.com/vrmarcelino/CCMetagen

https://spark.apache.org/docs/latest/

www.oracle.com/technetwork/java/index.html

https://github.com/laurikari/tre

plumed.github.io/doc-v2.0/user-doc/html/index.html

https://jupyter.readthedocs.io/en/latest/index.html

bowtie-bio.sourceforge.net/bowtie2/manual.shtml

https://healpix.sourceforge.io/

https://www.broadinstitute.org/haploview/haploview

scons.org/documentation.html

molevol.cmima.csic.es/castresana/Gblocks/Gblocks_documentat…

https://www.npmjs.com/

https://www.perl.org/docs.html

https://github.com/mummer4/mummer

www.repeatmasker.org/faq.html

https://www.freedesktop.org/wiki/Software/HarfBuzz/

https://github.com/rdpstaff/classifier

https://guertinlab.github.io/seqOutBias/seqOutBias_user_gui…

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