xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes

To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree reconciliation. While a number of software packages perform this type of analysis, none are...

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Autores principales: Liu, Nuo, Gonzalez, Tonatiuh A., Fischer, Jacob, Hong, Chan, Johnson, Michelle, Mawhorter, Ross, Mugnatto, Fabrizia, Soh, Rachael, Somji, Shifa, Wirth, Joseph S., Libeskind-Hadas, Ran, Bush, Eliot C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10362622/
https://www.ncbi.nlm.nih.gov/pubmed/37480009
http://dx.doi.org/10.1186/s12859-023-05410-0
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author Liu, Nuo
Gonzalez, Tonatiuh A.
Fischer, Jacob
Hong, Chan
Johnson, Michelle
Mawhorter, Ross
Mugnatto, Fabrizia
Soh, Rachael
Somji, Shifa
Wirth, Joseph S.
Libeskind-Hadas, Ran
Bush, Eliot C.
author_facet Liu, Nuo
Gonzalez, Tonatiuh A.
Fischer, Jacob
Hong, Chan
Johnson, Michelle
Mawhorter, Ross
Mugnatto, Fabrizia
Soh, Rachael
Somji, Shifa
Wirth, Joseph S.
Libeskind-Hadas, Ran
Bush, Eliot C.
author_sort Liu, Nuo
collection PubMed
description To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree reconciliation. While a number of software packages perform this type of analysis, none are geared toward a complete reconstruction for all families in an entire clade. Here we describe an update to the xenoGI software package which allows users to perform such an analysis using the newly developed DTLOR (duplication-transfer-loss-origin-rearrangement) reconciliation model starting from genome sequences as input.
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spelling pubmed-103626222023-07-23 xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes Liu, Nuo Gonzalez, Tonatiuh A. Fischer, Jacob Hong, Chan Johnson, Michelle Mawhorter, Ross Mugnatto, Fabrizia Soh, Rachael Somji, Shifa Wirth, Joseph S. Libeskind-Hadas, Ran Bush, Eliot C. BMC Bioinformatics Software To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers. A common approach is to perform a gene-tree / species-tree reconciliation. While a number of software packages perform this type of analysis, none are geared toward a complete reconstruction for all families in an entire clade. Here we describe an update to the xenoGI software package which allows users to perform such an analysis using the newly developed DTLOR (duplication-transfer-loss-origin-rearrangement) reconciliation model starting from genome sequences as input. BioMed Central 2023-07-21 /pmc/articles/PMC10362622/ /pubmed/37480009 http://dx.doi.org/10.1186/s12859-023-05410-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Liu, Nuo
Gonzalez, Tonatiuh A.
Fischer, Jacob
Hong, Chan
Johnson, Michelle
Mawhorter, Ross
Mugnatto, Fabrizia
Soh, Rachael
Somji, Shifa
Wirth, Joseph S.
Libeskind-Hadas, Ran
Bush, Eliot C.
xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
title xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
title_full xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
title_fullStr xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
title_full_unstemmed xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
title_short xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
title_sort xenogi 3: using the dtlor model to reconstruct the evolution of gene families in clades of microbes
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10362622/
https://www.ncbi.nlm.nih.gov/pubmed/37480009
http://dx.doi.org/10.1186/s12859-023-05410-0
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