News
Jan 2023: I am open to work as a part-time research scientist or contractor.
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.
Jun 2022: Paper by Joëlle Barido-Sottani, Tracy Heath, and lots of other people including me is published in the Bulletin of the Society of Systematic Biologists.
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
Since Sep 2015, I've been a research scientist with with Mark Holder on the Open Tree of Life project, part time.
After Nov 2022, I'll be open to work as a remote research scientist or contractor, part-time. I can do a wide variety of statistical and bioinformatics analyses, including read mapping, phylogeny and alignment estimation, and other statistical tests. I am also a good C++ programmer.
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.