Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages

SUMMARY: Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the p...

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Detalles Bibliográficos
Autores principales: Davín, Adrián A, Tricou, Théo, Tannier, Eric, de Vienne, Damien M, Szöllősi, Gergely J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7031779/
https://www.ncbi.nlm.nih.gov/pubmed/31566657
http://dx.doi.org/10.1093/bioinformatics/btz710
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author Davín, Adrián A
Tricou, Théo
Tannier, Eric
de Vienne, Damien M
Szöllősi, Gergely J
author_facet Davín, Adrián A
Tricou, Théo
Tannier, Eric
de Vienne, Damien M
Szöllősi, Gergely J
author_sort Davín, Adrián A
collection PubMed
description SUMMARY: Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree—species tree reconciliations. AVAILABILITY AND IMPLEMENTATION: Source code and manual are freely available in https://github.com/AADavin/ZOMBI/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-70317792020-02-25 Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages Davín, Adrián A Tricou, Théo Tannier, Eric de Vienne, Damien M Szöllősi, Gergely J Bioinformatics Applications Notes SUMMARY: Here we present Zombi, a tool to simulate the evolution of species, genomes and sequences in silico, that considers for the first time the evolution of genomes in extinct lineages. It also incorporates various features that have not to date been combined in a single simulator, such as the possibility of generating species trees with a pre-defined variation of speciation and extinction rates through time, simulating explicitly intergenic sequences of variable length and outputting gene tree—species tree reconciliations. AVAILABILITY AND IMPLEMENTATION: Source code and manual are freely available in https://github.com/AADavin/ZOMBI/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2020-02-15 2019-09-30 /pmc/articles/PMC7031779/ /pubmed/31566657 http://dx.doi.org/10.1093/bioinformatics/btz710 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Davín, Adrián A
Tricou, Théo
Tannier, Eric
de Vienne, Damien M
Szöllősi, Gergely J
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
title Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
title_full Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
title_fullStr Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
title_full_unstemmed Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
title_short Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
title_sort zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7031779/
https://www.ncbi.nlm.nih.gov/pubmed/31566657
http://dx.doi.org/10.1093/bioinformatics/btz710
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