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539locusturtle

afterqc

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

ambystomacapture

Analysis scripts and data relating to "Exon Capture Optimization in Large-Genome Amphibians"

arc

Assembly by Reduced Complexity (ARC)

clustopt

Scripts for the optimization of RADseq clustering thresholds in population genetics

cpwp

Program to infer pairwise pi among individuals using aligned short-read sequencing data.

ctsprobes

Analysis scripts for "Exon Capture Optimization in Large-Genome Amphibians (Ambystoma spp.)"

frogpipe

Bioinformatics pipeline to be tested on frogs Illumina run

frogpipe2

Frogpipe reboot

garynewts

Data processing pipeline for Gary's newts on maven

herpseqgrowth

Code for data aggregation and figure generation for our review in Annual Reviews of Animal Biosciences

mandercap

mandercap2

mitonuc

modernphylogeny

Aggregate DNA data from NCBI, analyze, and publish online phylognies

ngstools

NGSTools

pyrad

Assembly and analysis of RADseq data sets

redpill

OS X screen saver of scrolling green A's, T's, C's, and G's

reptileamphibianseqgrowth

Code for data aggregation and figure generation for our review in Annual Reviews of Animal Biosciences

shinycts

snps2alleles

Script for converting biallelic individual SNP genotype data into per-locus population-level allele count data for use with TreeMix

splicefinder

testnotebook

tortgen

tortgen2

Desert tortoise data processing on maven

tortqc

QC for desert tortoise

turtlebackbone

vcftohaploytypetrees

Starting with a phased (e.g. with beagle) VCF, parse into independent loci, build alignment files with reference, pull in ax/tig data, build trees, and visualize

velvettarget

Optimize kmer choice for velvet in target enrichment experiments.

vim

vim-configs