Historian: accurate reconstruction of ancestral sequences and evolutionary rates

نویسنده

  • Ian Holmes
چکیده

Motivation Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Results Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Availability and Implementation Historian is available at https://github.com/evoldoers/historian under the Creative Commons Attribution 3.0 US license. Contact [email protected].

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عنوان ژورنال:
  • Bioinformatics

دوره 33 8  شماره 

صفحات  -

تاریخ انتشار 2017