faircloth-lab/illumiprocessor

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Created almost 13 years ago
Updated about 2 years ago

faircloth-lab/illumiprocessor

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pre-process illumina reads

phyluce

software for UCE (and general) phylogenomics

edittag

edit distance sequence tags and helpers

protocols

Our laboratory repository

seqtools

Tools for sequence and alignment manipulation

splitaake

demultiplex massively parallel sequencing data

bird-db

the application and database underlying birds.faircloth-lab.org

tapir

Tally Approximations of Phylogenetic Informativeness Rapidly (TAPIR)

conda-recipes

bioinformatics program recipes for the conda package manager

demuxipy

Locate, error-correct, trim, and organize (hierarchically) sequence-tagged next-generation DNA reads

uce-probe-sets

Repository of different outgroup databases for use building UCE trees

itero

A strongly opinionated, iterative, guided contig assembly pipeline. Integrates (+error-correction), bwa-mem, bedtools, and samtools. MPI and multiprocessing aware.

uce-probe-design

Code for designing UCE probes

mod-primer3

modified primer3 version that tracks primer3.sourceforge.net trunk

colony2-helpers

code to help run colony2

mp-est

modified version of mpest with CLI parameters

data-theme

msatcommander-gs

A grown-up version of msatcommander for genome-scale data

pd-ht

dimensions

Code associated with our NSF Dimensions of Biodiversity grant

radcap

Software for processing data from RADcap

cookiecutter-supermike-examl

2011-fairclothetal-systbiol-uce

[Unsupported] Code used in Faircloth et al. Ultraconserved Elements Anchor Genetics Markers