RT Journal Article
SR Electronic
T1 Historian: accurate reconstruction of ancestral sequences and evolutionary rates
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 093161
DO 10.1101/093161
A1 Ian Holmes
YR 2016
UL http://biorxiv.org/content/early/2016/12/11/093161.abstract
AB 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. 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. Historian is available at https://github.com/ihh/indelhistorian under the Creative Commons Attribution 3.0 US license. Contact: Ian Holmes ihholmes+historian{at}gmail.com.