Software

I generally write software for high performance computing UNIX systems, primarily Linux and OS X, and develop code in Perl, C, C++ and R — depending on the needs of individual applications.

My group and I have extensively tested and validated the following programs, but software is never completely bug free. As always, interpret your results critically. I would appreciate hearing from you if you find an error. This caveat aside, my code is freely available for research use.

SolexaQA

illumina

SolexaQA creates statistics and visual representations of data quality for Illumina next generation sequencing data.


HyLiTE

hylite

HyLiTE analyzes gene-expression transcriptome data from hybrid and allopolyploid species.


IMgc

recombination

IMgc generates recombination-free sequences from recombination-rich multiple sequence alignments.


Adwave

adwave

Adwave implements wavelet analysis to infer local ancestry along the chromosomes in admixed populations.


SMARTPOP

smartpop

SMARTPOP is a fast population genetics simulator, especially designed to model social behavior and mating rules.


Recomb Package

ancestral recombination graph

The recomb package simulates and summarizes genetic datasets with recombination rates that change over time.


Microsat

microsatelites

Microsat simulates the evolution of linked and unlinked microsatellites using the coalescent.


Drifter

frequencies

Drifter simulates allele frequencies using forward-in-time evolution under the Wright-Fisher model.