TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structural...

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Main Authors: Chang, Jia-Ming, Di Tommaso, Paolo, Lefort, Vincent, Gascuel, Olivier, Notredame, Cedric
Format: Online
Language:English
Published: Oxford University Press 2015
Online Access:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489230/
id pubmed-4489230
recordtype oai_dc
spelling pubmed-44892302015-07-07 TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction Chang, Jia-Ming Di Tommaso, Paolo Lefort, Vincent Gascuel, Olivier Notredame, Cedric Web Server issue This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs. Oxford University Press 2015-07-01 2015-04-08 /pmc/articles/PMC4489230/ /pubmed/25855806 http://dx.doi.org/10.1093/nar/gkv310 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. 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.
repository_type Open Access Journal
institution_category Foreign Institution
institution US National Center for Biotechnology Information
building NCBI PubMed
collection Online Access
language English
format Online
author Chang, Jia-Ming
Di Tommaso, Paolo
Lefort, Vincent
Gascuel, Olivier
Notredame, Cedric
spellingShingle Chang, Jia-Ming
Di Tommaso, Paolo
Lefort, Vincent
Gascuel, Olivier
Notredame, Cedric
TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
author_facet Chang, Jia-Ming
Di Tommaso, Paolo
Lefort, Vincent
Gascuel, Olivier
Notredame, Cedric
author_sort Chang, Jia-Ming
title TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
title_short TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
title_full TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
title_fullStr TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
title_full_unstemmed TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
title_sort tcs: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
description This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. The evaluation can be used to identify the aligned positions most likely to contain structurally analogous residues and also most likely to support an accurate phylogenetic reconstruction. The TCS scoring scheme has been shown to be accurate predictor of structural alignment correctness among commonly used methods. It has also been shown to outperform common filtering schemes like Gblocks or trimAl when doing MSA post-processing prior to phylogenetic tree reconstruction. The web server is available from http://tcoffee.crg.cat/tcs.
publisher Oxford University Press
publishDate 2015
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4489230/
_version_ 1613243082082353152

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