OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes

We present version 10 of OrthoMaM, a database of orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments and phylogenetic trees of high-quality computed with state-of-the-art methods on up-to-date data. The main contribution...

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Autores principales: Scornavacca, Celine, Belkhir, Khalid, Lopez, Jimmy, Dernat, Rémy, Delsuc, Frédéric, Douzery, Emmanuel J P, Ranwez, Vincent
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Resources
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445298/
https://www.ncbi.nlm.nih.gov/pubmed/30698751
http://dx.doi.org/10.1093/molbev/msz015
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author Scornavacca, Celine
Belkhir, Khalid
Lopez, Jimmy
Dernat, Rémy
Delsuc, Frédéric
Douzery, Emmanuel J P
Ranwez, Vincent
author_facet Scornavacca, Celine
Belkhir, Khalid
Lopez, Jimmy
Dernat, Rémy
Delsuc, Frédéric
Douzery, Emmanuel J P
Ranwez, Vincent
author_sort Scornavacca, Celine
collection PubMed
description We present version 10 of OrthoMaM, a database of orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments and phylogenetic trees of high-quality computed with state-of-the-art methods on up-to-date data. The main contribution of this version is the increase in the number of taxa: 116 mammalian genomes for 14,509 one-to-one orthologous genes. This has been made possible by the combination of genomic data deposited in Ensembl complemented by additional good-quality genomes only available in NCBI. Version 10 users will benefit from pipeline improvements and a completely redesigned web-interface.
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spelling pubmed-64452982019-04-05 OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes Scornavacca, Celine Belkhir, Khalid Lopez, Jimmy Dernat, Rémy Delsuc, Frédéric Douzery, Emmanuel J P Ranwez, Vincent Mol Biol Evol Resources We present version 10 of OrthoMaM, a database of orthologous mammalian markers. OrthoMaM is already 11 years old and since the outset it has kept on improving, providing alignments and phylogenetic trees of high-quality computed with state-of-the-art methods on up-to-date data. The main contribution of this version is the increase in the number of taxa: 116 mammalian genomes for 14,509 one-to-one orthologous genes. This has been made possible by the combination of genomic data deposited in Ensembl complemented by additional good-quality genomes only available in NCBI. Version 10 users will benefit from pipeline improvements and a completely redesigned web-interface. Oxford University Press 2019-04 2019-01-29 /pmc/articles/PMC6445298/ /pubmed/30698751 http://dx.doi.org/10.1093/molbev/msz015 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Resources
Scornavacca, Celine
Belkhir, Khalid
Lopez, Jimmy
Dernat, Rémy
Delsuc, Frédéric
Douzery, Emmanuel J P
Ranwez, Vincent
OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes
title OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes
title_full OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes
title_fullStr OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes
title_full_unstemmed OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes
title_short OrthoMaM v10: Scaling-Up Orthologous Coding Sequence and Exon Alignments with More than One Hundred Mammalian Genomes
title_sort orthomam v10: scaling-up orthologous coding sequence and exon alignments with more than one hundred mammalian genomes
topic Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6445298/
https://www.ncbi.nlm.nih.gov/pubmed/30698751
http://dx.doi.org/10.1093/molbev/msz015
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