It was great to see old friends and meet new people at the Evolution 2023 meeting in Albuquerque, New Mexico!
I gave a talk on the effects of divergence on the effectiveness of read mapping and subsequent variant calling. You can check out the slides from my talk
here.
degenotateAnnotate the degeneracy of coding sites in a genome and extract coding sequences of specified
degeneracy. Also counts synonymous and nonysnonymous changes within and between populations to perform a basic
MK test. Included in
the snpArchervariant calling workflow.
PhyloAccSubstitution rate shifts in non-coding DNA.
A Bayesian framework to estimate substitution rates in non-coding DNA elements,
developed in Hu et al. 2019.
Version 2 now accounts for phylogenetic discordance.
pseudo-itReference-based genome assembly with iterative read mapping to alleviate reference bias.
Software developed
in the Good lab
to reduce reference bias in reference-based genome assembly
using an iterative mapping process to generate pseudo-genomes.
RefereeReference assembly quality scores.
Using genotype likelihoods from reads mapped back to an assembly, Referee assigns a
quality score to every position of that assembly. Developed in
Thomas and Hahn 2019.
GRAMPAGene-tree Reconciliation Algorithm with MUL-trees for Polyploid Analysis.
Software to identify polyploidy events given a species tree and a set of gene trees. Can count
duplications and losses in the presence of polyploidy and differentiate between auto- and
allopolyploidy events. Developed in
Thomas et al. 2017.
CAFEComputational Analysis of Gene Family Evolution.
Software developed in the Hahn lab
to estimate rates of gene family evolution and reconstruct ancestral gene counts. I contributed version 3.
GWCTGenome-Wide Convergence Tester.
These scripts and earlier versions of them were used in
Foote et al. 2015,
Thomas and Hahn 2015,
and Thomas et al. 2017
to count convergent and divergent substitutions in a phylogeny. No longer maintained.
CORECOde for Romps in Evolutionary data.
My personal scripts and libraries for manipulating sequence data, phylogenetic trees, and other things.
Best acronym.
Project resources
ArthroFam.org
A website I built to browse phylogenetic, gene family, and protein domain results of 76 arthropod species as part of the
i5K pilot project.
Macaque CNVs
Code and data used to produce the figures in our rhesus macaque CNV
paper.
Owl monkey mutations -
Github
A markdown document to accompany our paper
on mutation rates in owl monkeys. Goes through our analyses and provides code for reproducible figures.
