Our research group is committed to providing all our software and data free and open-source.
Lab Software Projects
BADGER (Bivariate Analysis of Differential Gene Expression Reactions) is a software package for studying the evolution of a control-treatment time series RNA-Seq experiment to explicitly contrast control and treatment differences to a differential gene reaction test.
MVFtools is a toolkit for multi-genomic and multi-transcriptomic dataset analysis. MVFtools can convert VCF, Phylip, and FASTA alignments data to a versatile compressed MVF file that can be used to generate window-based phylogenies, chromosomal plots, compute summary statistics, and calculate D-statistics over several organismal groups.
PhyDGET is a tool for transforming RNA-seq data for parallel analysis using BayesTraits to perform branch-specific tests of expression shift.
DFOIL converts FASTA alignments to a table of bialleic pattern counts and conducts an integrated set of four ABBA-BABA tests (DFOIL) that can determine directional patterns of introgression for a five taxon symmetric tree.
Quartet Sampling is a parellelized Python-based program that rapidly computes branch support scores by sampling quartets spanning each branch in a given phylogeny. The statistics provided by QS are specifically designed to disentangle scenarios of low information from conflicting information. QS works particularly well for large-sparse alignments or genome-wide alignments with strong conflict due to ILS or introgression. QS also performs well on standard single gene and multigene alignment phylogenies.
mixTape (mix of Tools for Analysis in Phylogenetics and Evolution) is a set of miscellaneous useful Python tools we have developed to perform various data manipulations associated with phylogenetics and molecular evolution data analysis.