Our research group is committed to providing all our software and data free and open-source. Below you can find links to our software projects and other software that we use in the lab.
Lab Software Projects
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. However, QS also performs well on standard single- and multi-gene 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.