Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

Simon Penel; Hugo Menet; Théo Tricou; Vincent Daubin; Eric Tannier

doi:10.1093/bioinformatics/btac062

Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation

Bioinformatics. 2022 Apr 12;38(8):2350-2352. doi: 10.1093/bioinformatics/btac062.

Authors

Simon Penel¹, Hugo Menet¹, Théo Tricou¹, Vincent Daubin¹, Eric Tannier^{1

2}

Affiliations

¹ Laboratoire de Biométrie et Biologie Evolutive/UMR5558, CNRS/UCBL, Villeurbanne 69622, France.
² Centre de Recherche Inria Lyon, Villeurbanne 69622, France.

PMID: 35139153
DOI: 10.1093/bioinformatics/btac062

Abstract

Motivation: Reconciliation between a host and its symbiont phylogenies or between a species and a gene phylogenies is a prevalent approach in evolution, however no simple generic tool (i.e. virtually usable by all reconciliation software, from host/symbiont to species/gene comparisons) is available to visualize reconciliation results. Moreover there is no tool to visualize 3-levels reconciliations, i.e. to visualize 2 nested reconciliations as for example in a host/symbiont/gene complex.

Results: Thirdkind is a light and easy to install command line software producing svg files displaying reconciliations, including 3-levels reconciliations. It takes a standard format recPhyloXML as input, and is thus usable with most reconciliation software.

Availability and implementation: https://github.com/simonpenel/thirdkind/wiki.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Phylogeny
Software*