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links.rst
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.. _phyluce: https://github.com/faircloth-lab/phyluce
.. _illumiprocessor: https://github.com/faircloth-lab/illumiprocessor/
.. _screen: http://www.gnu.org/software/screen/
.. _tmux: http://tmux.sourceforge.net/
.. _gzip: http://www.gzip.org/
.. _Casava: http://support.illumina.com/sequencing/sequencing_software/casava.ilmn
.. _bcl2fastq: https://support.illumina.com/downloads/bcl2fastq_conversion_software_184.ilmn
.. _fastx-toolkit: http://hannonlab.cshl.edu/fastx_toolkit/
.. _bartab: http://www.phyloware.com/Phyloware/XSTK.html
.. _velvet: http://www.ebi.ac.uk/~zerbino/velvet/
.. _ABySS: http://www.bcgsc.ca/platform/bioinfo/software/abyss
.. _Trinity: http://trinityrnaseq.sourceforge.net/
.. _homebrew: http://mxcl.github.com/homebrew/
.. _Amazon Web Services: http://aws.amazon.com/
.. _IDTDNA: http://www.idtdna.com/site
.. _uce-probe-sets: https://github.com/faircloth-lab/uce-probe-sets
.. _CloudForest: https://github.com/ngcrawford/CloudForest
.. _sqlite: http://www.sqlite.org
.. _sqlite-tutorial: http://www.sqlite.org/sqlite.html
.. _github: https://github.com/faircloth-lab/phyluce
.. _conda: http://docs.continuum.io/conda/
.. _multiprocessing: http://docs.python.org/2/library/multiprocessing.html
.. _Tree of Life: http://en.wikipedia.org/wiki/Tree_of_Life
.. _Phylogenomics: http://en.wikipedia.org/wiki/Phylogenomics
.. _CLI: http://en.wikipedia.org/wiki/Command-line_interface
.. _RAD-seq: http://en.wikipedia.org/wiki/Restriction_site_associated_DNA_markers
.. _RNA-seq: http://en.wikipedia.org/wiki/RNA-Seq
.. _amplicon sequencing: http://www.ncbi.nlm.nih.gov/pubmed/18274529
.. _unittests: http://en.wikipedia.org/wiki/Unit_testing
.. _Python: http://www.python.org
.. _cli branch: https://github.com/faircloth-lab/phyluce/tree/cli
.. _anaconda: http://docs.continuum.io/anaconda/install.html
.. _miniconda: http://repo.continuum.io/miniconda/
.. _CC-BY: http://creativecommons.org/licenses/by/4.0/
.. _virtualenv: http://www.virtualenv.org/
.. _MiSeq: http://www.illumina.com/systems/miseq.ilmn
.. _HiSeq: http://www.illumina.com/systems/hiseq_2500_1500.ilmn
.. _Illumina: http://www.illumina.com/
.. _lastz: http://www.bx.psu.edu/~rsharris/lastz/
.. _relational database: http://en.wikipedia.org/wiki/Relational_database
.. _FastQC: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
.. _symlinks: http://en.wikipedia.org/wiki/Symbolic_link
.. _symlink: http://en.wikipedia.org/wiki/Symbolic_link
.. _raxml: http://sco.h-its.org/exelixis/web/software/raxml/index.html
.. _exabayes: http://sco.h-its.org/exelixis/web/software/examl/index.html
.. _examl: http://sco.h-its.org/exelixis/web/software/exabayes/index.html
.. _mafft: http://mafft.cbrc.jp/alignment/software/
.. _muscle: http://www.drive5.com/muscle/
.. _gblocks: http://molevol.cmima.csic.es/castresana/Gblocks.html
.. _UCSC Genome Browser: https://genome.ucsc.edu/
.. _UCSC Genome Browser Downloads: https://genome.ucsc.edu/downloads
.. _Kent Source Archive: http://hgdownload.soe.ucsc.edu/admin/exe/
.. _NCBI: http://www.ncbi.nlm.nih.gov/
.. _stampy: http://www.well.ox.ac.uk/project-stampy
.. _samtools: http://www.htslib.org/
.. _BED: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
.. _bedtools: http://bedtools.readthedocs.io/en/latest/
.. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf
.. _SAM: https://samtools.github.io/hts-specs/SAMv1.pdf
.. _Applied Genetics Laboratories: http://www.appliedgenetics.com/products/hybloc-competitor-dna/
.. _NCBI BioProject: https://www.ncbi.nlm.nih.gov/bioproject/
.. _bioconda: https://bioconda.github.io
.. _canu: https://github.com/marbl/canu
.. _longranger: https://support.10xgenomics.com/genome-exome/software/pipelines/latest/installation
.. _arks: https://github.com/bcgsc/arks
.. _links: https://github.com/bcgsc/LINKS
.. _tigmint: https://github.com/bcgsc/tigmint
.. _10X: https://www.10xgenomics.com
.. _Pilon: https://github.com/broadinstitute/pilon/wiki
.. _raxml-ng: https://github.com/amkozlov/raxml-ng
.. _cactus: https://github.com/ComparativeGenomicsToolkit/cactus
.. _boto: http://boto.cloudhackers.com/en/latest/
.. _toil: https://github.com/DataBiosphere/toil
.. _aws: https://aws.amazon.com
.. _ec2: https://aws.amazon.com/ec2/
.. _GATK: https://gatk.broadinstitute.org/hc/en-us
.. _BBmap: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmap-guide/
.. _Stacks: https://catchenlab.life.illinois.edu/stacks/