faircloth-lab/protocols

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faircloth-lab/protocols

faircloth-lab

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Our laboratory repository

phyluce

software for UCE (and general) phylogenomics

illumiprocessor

pre-process illumina reads

edittag

edit distance sequence tags and helpers

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