• Bali-Phy version 3: Model-based co-estimation of alignment and phylogeny

    1 month ago - By Oxford Journals

    AbstractSummaryWe describe improvements to BAli-Phy, a Markov chain Monte Carlo program that jointly estimates phylogeny, alignment, and other parameters from unaligned sequence data. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models, and other new models. It implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously.AvailabilitySoftware is available for download at. C++ source code is freely available on Github under the GPL2 License.
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