title: TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction.
abstract: 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.
authors: Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institute of Human Genetics (IGH), UPR 1142, CNRS, 34396 Montpellier, France.
authors: Jia-Ming
authors: http://orcid.org/0000-0002-6711-1739
authors: JM
authors: Chang
authors: Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain.
authors: Paolo
authors: P
authors: Di Tommaso
authors: Institut de Biologie Computationnelle, LIRMM, UMR 5506: CNRS & Université de Montpellier, France.
authors: Vincent
authors: V
authors: Lefort
authors: Institut de Biologie Computationnelle, LIRMM, UMR 5506: CNRS & Université de Montpellier, France.
authors: Olivier
authors: O
authors: Gascuel
authors: Comparative Bioinformatics, Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain cedric.notredame@crg.eu.
authors: Cedric
authors: C
authors: Notredame
mesh_terms: D000465:Algorithms; D020407:Internet; D010802:Phylogeny; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software