Software we've created
As part of our research, we create software tools to help distill information from genomic data. We always make these tools freely available to other investigators, and hope that they make analyses faster, more accurate, and more reproducible.
pixy
Unbiased estimation of nucleotide diversity and divergence with missing data
Co-developed with Dr. Katharine Korunes, pixy is a command-line tool for painlessly and correctly estimating average nucleotide diversity within (π) and between (dxy) populations from a VCF. In particular, pixy facilitates these calculations using VCFs containing invariant sites, missing sites, and missing genotypes.
For more information see:Our manuscript describing pixy
Github repo with installation instructions
Full documentation
syntR
Reproducible identification of chromosomal rearrangements
Co-developed with Dr. Kate Ostevik, syntR is an R package for the reproducible identification of synteny blocks and chromosomal rearrangments via comparison of two genetic maps. syntR implements an error-aware clustering algorithm specifically designed for the highly linear structure of comparative genetic map data. syntR can be used to identify synteny blocks using any type of ordered genetic markers.
For more information see:Our manuscript describing syntR
Github repo with installation instructions
Full documentation