title: T-Coffee: Tree-based consistency objective function for alignment evaluation.
abstract: T-Coffee, for Tree-based consistency objective function for alignment evaluation, is a versatile multiple sequence alignment (MSA) method suitable for aligning virtually any type of biological sequences. T-Coffee provides more than a simple sequence aligner; rather it is a framework in which alternative alignment methods and/or extra information (i.e., structural, evolutionary, or experimental information) can be combined to reach more accurate and more meaningful MSAs. T-Coffee can be used either by running input data via the Web server ( http://tcoffee.crg.cat/apps/tcoffee/index.html ) or by downloading the T-Coffee package. Here, we present how the package can be used in its command line mode to carry out the most common tasks and multiply align proteins, DNA, and RNA sequences. This chapter particularly emphasizes on the description of T-Coffee special flavors also called "modes," designed to address particular biological problems.
authors.affiliation: Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Cedrik
authors.initials: C
authors.lastname: Magis
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Taly
authors.forename: Giovanni
authors.initials: G
authors.lastname: Bussotti
authors.forename: Jia-Ming
authors.initials: JM
authors.lastname: Chang
authors.forename: Paolo
authors.initials: P
authors.lastname: Di Tommaso
authors.forename: Ionas
authors.initials: I
authors.lastname: Erb
authors.forename: José
authors.initials: J
authors.lastname: Espinosa-Carrasco
authors.forename: Cedric
authors.initials: C
authors.lastname: Notredame
mesh_terms: D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000235:genetics; D020407:Internet; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*
chemical_list: D011506:Proteins; D012313:RNA; D004247:DNA