Benjamin Redelings

Evolution, Computation, Statistics

Photo of Benjamin Redelings

News

Feb 2021: BAli-Phy 3.6 released!

Oct 2020: Preprint - BAli-Phy version 3: Model-based co-estimation of Alignment and Phylogeny

Jun 2018: Talk at SSB Satellite Meeting 2018 in Columbus, OH
"Taxonomic supertree construction with incertae sedis taxa"

Jun 2018: Poster at SSB Satellite Meeting 2018 in Columbus, OH
"Faster Likelihoods for Sparse Alignments"

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. Since Feb 2016, I've also been working with Greg Wray at Duke on malaria population genomics part time. I am currently applying the Sequential Markov Coalescent (SMC) to questions in malaria demography.

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
....310.......320.......330.......340.......350.......360.......370.......
Thermotoga DEVEIIGLSYEIKKTV---VTSVEMFRKELDEGIAGDNVGCLLRGIDKDEVERGQVLA-----APGSIKPHKRF
Anacystis ETIEIVGLR-DTRSTT---VTGVEMFQKTLDEGLAGDNVGLLLRGIQKTDIERGMVLA-----KPGSITPHTKF
Escheria EEVEIVGIK-ETQKST---CTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLA-----KPGTIKPHTKF
Pyrococcus EVVIFEPASTIFHKPIQGEVKSIEMHHEPLEEALPGDNIGFNVRGVSKNDIKRGDVAGHTTN-PPTVVRTKDTF
Halobacterium DNVSFQPSDVG------GEVKTIEMHHEEVPNAEPGDNVGFNVRGIGKDDIRRGDVCGPADD-PPSVA---DTF
Methanococcus DKVVFEPAGAI------GEIKTVEMHHEQLPSAEPGDNIGFNVRGVGKKDIKRGDVLGHTTN-PPTVA---TDF
Aeropyrum DKVVFMPPGVV------GEVRSIEMHYQQLQQAEPGDNIGFAVRGVSKSDIKRGDVAGHLDK-PPTVA---EEF
Sulfolobus DKIVFMPVGKI------GEVRSIETHHTKIDKAEPGDNIGFNVRGVEKKDVKRGDVAGSVQN-PPTVA---DEF
Giardia MKVVFAPTSQV------SEVKSVEMHHEELKKAGPGDNVGFNVRGLAVKDLKKGYVVGDVTNDPPVGC---KSF
Homo MVVTFAPVNVT------TEVKSVEMHHEALSEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEA---AGF
Euglena DVVTFAPNNLT------TEVKSVEMHHEALTEAVPGDNVGFNVKNVSVKDIRRGYVASNAKNDPAKEA---ADF
Nicotiana MVVTFGPTGLT------TEVKSVEMHHEALQEALPGDNVGFNVKNVAVKDLKRGFVASNSKDDPAKGA---ASF