A quality control analysis tool for high throughput sequencing data

Scripts for file processing and analysis in phylogenetics and phylogeography

Results from our project "Using ecological niche modeling to predict the response of Hydrocotyle bonariensis to global climate change"

Results from our project "Predicting the responses of Northern Gulf of Mexico coastal dune plant communities to climate change using ecological niche modeling"

Bagley Lab website

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

Automatically exported from code.google.com/p/cdhit

G-PhoCS is a software package for inferring ancestral population sizes, population divergence times, and migration rates from individual genome sequences.

Sequence simulator

Automatically exported from code.google.com/p/figtree

Shell scripting utility functions and a bash script boilerplate template

Utilities for automating bgc (Bayesian genomic cline) file prep, analysis, and results plotting

A system-level, binary package and environment manager running on all major operating systems and platforms.

Accurate Species TRee ALgorithm

Testing hybridization using species trees

Bioinformatic pipeline for processing Sequence Capture data for Phylogenetics

Should you cite this software?

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Recovering genes from targeted sequence capture data

Analyses done on sequence capture data from a Illumina HiSeq3000 and NextSeq, PE100 and PE150 respectively. The data were analyzed using the HybPiper pipeline

Successful Job Applications and Grants

a bash pipeline for RAD sequencing

A statistical framework for ploidy estimation using NGS short-read data

Exitwp is tool primarily aimed for making migration from one or more wordpress blogs to the jekyll blog engine as easy as possible.

The most popular HTML, CSS, and JavaScript framework for developing responsive, mobile first projects on the web.

Minimal tutorial on making a simple website with GitHub Pages

Semantic Versioning Specification

Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis

Automatically exported from code.google.com/p/densitree

Models for dealing with morphological data