Gregg Thomas

ctober 31, 2022

I was happy to give a workshop this week demonstrating PhyloAcc in Prof. Scott Edwards' comparative genomics class.

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July 13, 2022

After my talks in the spring, I launched a summer tour, giving talks and posters at multiple conferences! Check the Archive for more info about the tour dates, and the Publications & Talks page to download slides from all of my talks.

Archive

Substitution 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 gene tree discordance.

Pseudo 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.

Reference 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.

Gene-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.

Computational Analysis of Gene Family Evolution
Software developed in the Hahn lab to estimate rates of gene family evolution and reconstruct ancestral gene counts.

Genome-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.

COde for Romps in Evolutionary data
My personal scripts and libraries for manipulating sequence data, phylogenetic trees, and other things.

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.

Drosophila 25 species phylogeny
A FigShare micro-publication of the 25 species Drosophila phylogeny that was used to study gene families across the genus, in particular salivary glue genes.

Birds-of-paradise gene families
Results of gene family analyses in several species of birds-of-paradise. Paper.