Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information.

Autor:	Glez-Peña D; ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain.; CINBIO: Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain.; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain., López-Fernández H; ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain.; CINBIO: Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain.; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, 36213 Vigo, Spain., Duque P; Instituto de Investigação e Inovação em Saúde (I3S), 26706 Universidade do Porto , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.; Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.; Instituto de Ciências Biomédicas Abel Salazar (ICBAS), 26706 Universidade do Porto , Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.; Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal., Vieira CP; Instituto de Investigação e Inovação em Saúde (I3S), 26706 Universidade do Porto , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.; Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135 Porto, Portugal., Vieira J; Instituto de Investigação e Inovação em Saúde (I3S), 26706 Universidade do Porto , Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.; Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135 Porto, Portugal.
Jazyk:	angličtina
Zdroj:	Journal of integrative bioinformatics [J Integr Bioinform] 2024 Jul 24; Vol. 21 (2). Date of Electronic Publication: 2024 Jul 24 (Print Publication: 2024).
DOI:	10.1515/jib-2023-0051
Abstrakt:	When inferring the evolution of a gene/gene family, it is advisable to use all available coding sequences (CDS) from as many species genomes as possible in order to infer and date all gene duplications and losses. Nowadays, this means using hundreds or even thousands of CDSs, which makes the inferred phylogenetic trees difficult to visualize and interpret. Therefore, it is useful to have an automated way of collapsing large phylogenetic trees according to a taxonomic term decided by the user (family, class, or order, for instance), in order to highlight the minimal set of sequences that should be used to recapitulate the full history of the gene/gene family being studied at that taxonomic level, that can be refined using additional software. Here we present the Phylogenetic Tree Collapser (PTC) program (https://github.com/pegi3s/phylogenetic-tree-collapser), a flexible tool for automated tree collapsing using taxonomic information, that can be easily used by researchers without a background in informatics, since it only requires the installation of Docker, Podman or Singularity. The utility of PTC is demonstrated by addressing the evolution of the ascorbic acid synthesis pathway in insects. A Docker image is available at Docker Hub (https://hub.docker.com/r/pegi3s/phylogenetic-tree-collapser) with PTC installed and ready-to-run. (© 2024 the author(s), published by De Gruyter, Berlin/Boston.)
Databáze:	MEDLINE
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