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    48 repositories

    • phyluce

      Public
      software for UCE (and general) phylogenomics
      Python
      •
      Other
      •49•79•64•1•Updated Sep 5, 2024Sep 5, 2024

    • illumiprocessor

      Public
      pre-process illumina reads
      Python
      •
      Other
      •10•18•6•1•Updated Oct 27, 2022Oct 27, 2022

    • singularity

      Public
      Singularity Container Definition Files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 28, 2022Sep 28, 2022

    • cyverse

      Public
      Various Docker Files For CyVerse Discovery Environment
      Dockerfile
      •0•0•0•0•Updated Jun 3, 2021Jun 3, 2021

    • private-alleles

      Public
      Compute private alleles in one population relative to another
      Python
      •0•0•0•0•Updated Apr 6, 2021Apr 6, 2021

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.2k•0•0•0•Updated Feb 21, 2021Feb 21, 2021

    • edittag

      Public
      edit distance sequence tags and helpers
      Python
      •
      Other
      •4•12•2•3•Updated Feb 4, 2021Feb 4, 2021

    • protocols

      Public
      Our laboratory repository
      Python
      •
      BSD 2-Clause "Simplified" License
      •10•11•0•0•Updated Jan 12, 2021Jan 12, 2021

    • phyluce-workflows

      Public
      Snakemake workflows for phyluce tasks
      Python
      •0•0•0•0•Updated Nov 25, 2020Nov 25, 2020

    • cactus-prepare-parser

      Public
      A quick python script to generate SLURM submission scripts from `cactus-prepare` stdout
      Python
      •0•0•0•0•Updated Nov 24, 2020Nov 24, 2020

    • msatcommander-gs

      Public
      A grown-up version of msatcommander for genome-scale data
      Python
      •1•1•0•1•Updated Jul 24, 2020Jul 24, 2020

    • cactus

      Public
      Official home of genome aligner based upon notion of Cactus graphs
      C
      •
      Other
      •112•0•0•0•Updated Feb 7, 2020Feb 7, 2020

    • itero

      Public
      A strongly opinionated, iterative, guided contig assembly pipeline. Integrates (+error-correction), bwa-mem, bedtools, and samtools. MPI and multiprocessing aware.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•3•2•0•Updated Dec 21, 2018Dec 21, 2018

    • tapir

      Public
      Tally Approximations of Phylogenetic Informativeness Rapidly (TAPIR)
      Python
      •
      Other
      •0•6•3•0•Updated Jul 2, 2018Jul 2, 2018

    • radcap

      Public
      Software for processing data from RADcap
      Python
      •2•1•4•0•Updated May 29, 2018May 29, 2018

    • dockerfiles

      Public
      Docker files that we use
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 25, 2018Apr 25, 2018

    • threerad

      Public
      3RAD data processing
      MIT License
      •0•0•0•0•Updated Jan 10, 2018Jan 10, 2018

    • cookiecutter-supermike-examl

      Public
      Shell
      •2•1•0•0•Updated Dec 8, 2017Dec 8, 2017

    • index-counters

      Public
      Variety of Code for Counting Illumina Index Sequences
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 3, 2017Aug 3, 2017

    • chopsuey

      Public
      Virtual digests of DNA
      Python
      •0•0•0•0•Updated Jul 20, 2016Jul 20, 2016

    • conda-recipes

      Public
      bioinformatics program recipes for the conda package manager
      Python
      •
      Other
      •7•4•3•0•Updated Jun 16, 2015Jun 16, 2015

    • sate-core

      Public
      Python
      •3•0•0•0•Updated May 22, 2015May 22, 2015

    • splitaake

      Public
      demultiplex massively parallel sequencing data
      Python
      •
      Other
      •1•8•0•0•Updated Nov 25, 2014Nov 25, 2014

    • cookiecutter-supermike-exabayes

      Public
      Shell
      •0•0•0•0•Updated Oct 7, 2014Oct 7, 2014

    • meta

      Public
      Python
      •0•0•0•0•Updated Jul 23, 2014Jul 23, 2014

    • rhino

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jun 28, 2014Jun 28, 2014

    • sh_t

      Public
      parallel, automated SH-testing
      Python
      •
      Other
      •0•0•0•0•Updated Jun 23, 2014Jun 23, 2014

    • alfred_zotquery

      Public
      An Alfred workflow to interact with a user's Zotero data.
      AppleScript
      •11•0•0•0•Updated Jun 7, 2014Jun 7, 2014

    • uce-probe-design

      Public
      Code for designing UCE probes
      Python
      •
      Other
      •2•2•0•0•Updated May 6, 2014May 6, 2014

    • exa-helpers

      Public
      Python
      •0•0•0•0•Updated Mar 3, 2014Mar 3, 2014