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Updated: Oct 4, 2025

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Published on: August 14, 2018
Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation
Simon Penel1, Hugo Menet1, Théo Tricou1
1Laboratoire de Biométrie et Biologie Evolutive/UMR5558, CNRS/UCBL, Villeurbanne 69622, France.
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.
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