Incorporating indel information into phylogeny estimation for rapidly emerging pathogens |
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| Authors: | Benjamin D Redelings Marc A Suchard |
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| Institution: | (1) Bioinformatics Research Center, North Carolina State University, 27606 Raleigh, NC, USA;(2) Department of Biomathematics, David Geffen School of Medicine at UCLA, 90095 Los Angeles, CA, USA;(3) Department of Human Genetics, David Geffen School of Medicine at UCLA, 90095 Los Angeles, CA, USA;(4) Department of Biostatistics, UCLA Schoold of Public Health, 90095 Los Angeles, CA, USA |
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| Abstract: | Background Phylogenies of rapidly evolving pathogens can be difficult to resolve because of the small number of substitutions that accumulate
in the short times since divergence. To improve resolution of such phylogenies we propose using insertion and deletion (indel)
information in addition to substitution information. We accomplish this through joint estimation of alignment and phylogeny
in a Bayesian framework, drawing inference using Markov chain Monte Carlo. Joint estimation of alignment and phylogeny sidesteps
biases that stem from conditioning on a single alignment by taking into account the ensemble of near-optimal alignments. |
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