Benjamin Redelings

News

Jun 2015: BAli-Phy 2.3.7 released

Jun 2015 - Manuscript submitted to Genetics
"Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population." [arXiv]

Jun 2014: Talk at Evolution 2014
"Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population."

Jun 2014: Talk at iEvoBio 2014
"Probabilistic Programming for Evolutionary Biology."

Apr 2014: BAli-Phy 2.3 released
Faster, new model-specification language, more codon models and tests.

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

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