News
Oct 2023: Invited talk at Tulane University in New Orleans, LA: Alignments, rate variation, and heterotachy.
July 2023: Invited talk at SMBE2023 in Ferrara, Italy: Alignments, rate variation, and heterotachy.
Jan 2023: 2 presentations at SSB Satellite meeting in Mexico City. Helped lead an OpenTree workshop, and gave a lightning talk about speeding up the OpenTree synthesis algorithm by a factor of 550x or so.
Aug 2022: Paper by Tae Kun Seo, Jeff Thorne and me published in PNAS: "Correlations between alignment gaps and nucleotide substitution or amino acid replacement"
Jun 2022: Presentation Apicoplast phylogeny illuminates worldwide dispersal history of Plasmodium vivax at Evolution 2022 in Cleveland, OH.
Research
I use mathematics and computational techniques to answer questions in evolutionary genetics. The mathematics is mostly Bayesian inference and stochastic process modeling. The computation is primarily Markov chain Monte Carlo (MCMC). The evolutionary genetics has focused on phylogenetics and multiple sequence alignment, but recently includes some population genetics and coalescent theory as well.
Work
During 2024, I'm working with Xiang Ji as a (remote) Research Scientist at Tulane University. I'm working with Xiang to add action-based likelihood computation to the BEAGLE library, which will be helpful in large-state-space substitution models.
Phylogenetic Alignment
I develop the MCMC software BAli-Phy for inferring highly-accurate multiple sequence alignments (MSA). BAli-Phy performs inference under a phylogenetic model, and so it places insertions and deletions on specific branches of the evolutionary tree instead of just placing gaps in a matrix. BAli-Phy also co-estimates the evolutionary tree along with the alignment.
| uncertain certain |
| . | . | . | . | 3 | 1 | 0 | . | . | . | . | . | . | . | 3 | 2 | 0 | . | . | . | . | . | . | . | 3 | 3 | 0 | . | . | . | . | . | . | . | 3 | 4 | 0 | . | . | . | . | . | . | . | 3 | 5 | 0 | . | . | . | . | . | . | . | 3 | 6 | 0 | . | . | . | . | . | . | . | 3 | 7 | 0 | . | . | . | . | . | . | . | |
| Thermotoga | D | E | V | E | I | I | G | L | S | Y | E | I | K | K | T | V | - | - | - | V | T | S | V | E | M | F | R | K | E | L | D | E | G | I | A | G | D | N | V | G | C | L | L | R | G | I | D | K | D | E | V | E | R | G | Q | V | L | A | - | - | - | - | - | A | P | G | S | I | K | P | H | K | R | F |
| Anacystis | E | T | I | E | I | V | G | L | R | - | D | T | R | S | T | T | - | - | - | V | T | G | V | E | M | F | Q | K | T | L | D | E | G | L | A | G | D | N | V | G | L | L | L | R | G | I | Q | K | T | D | I | E | R | G | M | V | L | A | - | - | - | - | - | K | P | G | S | I | T | P | H | T | K | F |
| Escheria | E | E | V | E | I | V | G | I | K | - | E | T | Q | K | S | T | - | - | - | C | T | G | V | E | M | F | R | K | L | L | D | E | G | R | A | G | E | N | V | G | V | L | L | R | G | I | K | R | E | E | I | E | R | G | Q | V | L | A | - | - | - | - | - | K | P | G | T | I | K | P | H | T | K | F |
| Pyrococcus | E | V | V | I | F | E | P | A | S | T | I | F | H | K | P | I | Q | G | E | V | K | S | I | E | M | H | H | E | P | L | E | E | A | L | P | G | D | N | I | G | F | N | V | R | G | V | S | K | N | D | I | K | R | G | D | V | A | G | H | T | T | N | - | P | P | T | V | V | R | T | K | D | T | F |
| Halobacterium | D | N | V | S | F | Q | P | S | D | V | G | - | - | - | - | - | - | G | E | V | K | T | I | E | M | H | H | E | E | V | P | N | A | E | P | G | D | N | V | G | F | N | V | R | G | I | G | K | D | D | I | R | R | G | D | V | C | G | P | A | D | D | - | P | P | S | V | A | - | - | - | D | T | F |
| Methanococcus | D | K | V | V | F | E | P | A | G | A | I | - | - | - | - | - | - | G | E | I | K | T | V | E | M | H | H | E | Q | L | P | S | A | E | P | G | D | N | I | G | F | N | V | R | G | V | G | K | K | D | I | K | R | G | D | V | L | G | H | T | T | N | - | P | P | T | V | A | - | - | - | T | D | F |
| Aeropyrum | D | K | V | V | F | M | P | P | G | V | V | - | - | - | - | - | - | G | E | V | R | S | I | E | M | H | Y | Q | Q | L | Q | Q | A | E | P | G | D | N | I | G | F | A | V | R | G | V | S | K | S | D | I | K | R | G | D | V | A | G | H | L | D | K | - | P | P | T | V | A | - | - | - | E | E | F |
| Sulfolobus | D | K | I | V | F | M | P | V | G | K | I | - | - | - | - | - | - | G | E | V | R | S | I | E | T | H | H | T | K | I | D | K | A | E | P | G | D | N | I | G | F | N | V | R | G | V | E | K | K | D | V | K | R | G | D | V | A | G | S | V | Q | N | - | P | P | T | V | A | - | - | - | D | E | F |
| Giardia | M | K | V | V | F | A | P | T | S | Q | V | - | - | - | - | - | - | S | E | V | K | S | V | E | M | H | H | E | E | L | K | K | A | G | P | G | D | N | V | G | F | N | V | R | G | L | A | V | K | D | L | K | K | G | Y | V | V | G | D | V | T | N | D | P | P | V | G | C | - | - | - | K | S | F |
| Homo | M | V | V | T | F | A | P | V | N | V | T | - | - | - | - | - | - | T | E | V | K | S | V | E | M | H | H | E | A | L | S | E | A | L | P | G | D | N | V | G | F | N | V | K | N | V | S | V | K | D | V | R | R | G | N | V | A | G | D | S | K | N | D | P | P | M | E | A | - | - | - | A | G | F |
| Euglena | D | V | V | T | F | A | P | N | N | L | T | - | - | - | - | - | - | T | E | V | K | S | V | E | M | H | H | E | A | L | T | E | A | V | P | G | D | N | V | G | F | N | V | K | N | V | S | V | K | D | I | R | R | G | Y | V | A | S | N | A | K | N | D | P | A | K | E | A | - | - | - | A | D | F |
| Nicotiana | M | V | V | T | F | G | P | T | G | L | T | - | - | - | - | - | - | T | E | V | K | S | V | E | M | H | H | E | A | L | Q | E | A | L | P | G | D | N | V | G | F | N | V | K | N | V | A | V | K | D | L | K | R | G | F | V | A | S | N | S | K | D | D | P | A | K | G | A | - | - | - | A | S | F |
Fixed-Alignment Phylogenetic Inference
I've also been contributing to RevBayes, a general program for Bayesian phylogenetic inference.