Benjamin Redelings

News

Apr 2014: BAli-Phy 2.3 released
Speed improvements, add more codon models.

Apr 2014 - Manuscript accepted in MBE
"Erasing Errors Due to Alignment Ambiguity When Estimating Positive Selection" (PDF)

Dec 2013: BAli-Phy 2.2 released
Successfully accounts for alignment uncertainty in testing for (diversifying) positive selection.

Aug 2013 - Seminar at NCSU
"Multi-connected graphs, partial splits, and wandering taxa: representing phylogenetic uncertainty".

Aug 2013 - Talk at JSM 2013
"Erasing Errors due to Alignment Ambiguity when inferring (diversifying) positive selection".

Jul 2013 - Invited talk at SMBE 2013 (joint work with Marcy)
"Bayesian Co-estimation of Selfing Rate and Locus-Specific Mutation Rates for a Partially Selfing Population"

Oct 2012 - Started a postdoc at Duke University
Working with Dr. Marcy Uyenoyama on problems related to coalescent theory.

I am interested in mathematical and computational modelling of stochastic processes in all areas of biology. I focus primarily on evolutionary genetics. I work on Bayesian inference, and on phylogenetics and alignment estimation using MCMC. I am currently exploring coalescent theory, designing new models and inference algorithms. I am also exploring a Turing-complete extension of graphical models, called probabilistic programming.

I also develop the software BAli-Phy (and tools):

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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