PastView: a user-friendly interface to explore ancestral scenarios

BMC Evolutionary Biology
François ChevenetOlivier Gascuel

Abstract

Ancestral character states computed from the combination of phylogenetic trees with extrinsic traits are used to decipher evolutionary scenarios in various research fields such as phylogeography, epidemiology, and ecology. Despite the existence of powerful methods and software in ancestral character state inference, difficulties may arise when interpreting the outputs of such inferences. The growing complexity of data (trees, annotations), the diversity of optimization criteria for computing trees and ancestral character states, the combinatorial explosion of potential evolutionary scenarios if some ancestral characters states do not stand out clearly from others, requires the design of new methods to explore associations of phylogenetic trees with extrinsic traits, to ease the visualization and interpretation of evolutionary scenarios. We developed PastView, a user-friendly interface that includes numerical and graphical features to help users to import and/or compute ancestral character states from discrete variables and extract ancestral scenarios as sets of successive transitions of character states from the tree root to its leaves. PastView provides summarized views such as transition maps and integrates comparative tools ...Continue Reading

References

Jan 1, 1981·Journal of Molecular Evolution·J Felsenstein
Jun 1, 2000·Molecular Biology and Evolution·T PupkoD Graur
Jan 22, 2004·Bioinformatics·Emmanuel ParadisKorbinian Strimmer
Mar 1, 2006·BMC Bioinformatics·Jonathan P Bollback
Sep 12, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yun CuiWing-Kin Sung
Jan 19, 2013·Bioinformatics·François ChevenetOlivier Gascuel
Jan 15, 2014·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Atul M WalimbeSarah S Cherian
May 18, 2016·Molecular Biology and Evolution·Filip BielejecPhilippe Lemey
Jun 27, 2018·Virus Evolution·Marc A SuchardAndrew Rambaut
May 28, 2019·Molecular Biology and Evolution·Sohta A IshikawaOlivier Gascuel

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Citations

Sep 29, 2021·BMC Bioinformatics·François ChevenetAnne-Laure Bañuls

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Software Mentioned

DELTRAN
R
Tcl
SpreaD3
PastView MAP
NEXUS
PhyloType
Windows
MAP
Tk

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