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.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

“…Briefly, the longest encoded protein for each gene was subjected to an all-versus-all NCBI BLAST + alignment followed by clustering with hcluster_sg 130 . Each cluster, regarded as a gene family, was subjected to multiple-sequence alignment using several independent methods [131][132][133][134] , with a consensus alignment produced with M-Coffee 135 . TreeBest software was used to construct consensus phylogenetic gene trees incorporating five different tree-building methods: two were maximum-likelihood methods based on either protein alignment (WAG model) or codon alignment (phymal HKY model), and three were neighbor-joining methods that used p distance, dN distance or dS distance within codon alignments.…”

A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium

“…We then performed multiple sequence alignment of the candidate M. genitalium drug targets, their bacterial homologs with known inhibitors, and their human homologs. We performed this using TCoffee version 11.00.8cbe486 (Magis et al, 2014) with the default settings. We inspected the sequence alignment to verify that the reported binding sites are conserved among bacteria and divergent with humans.…”

Alignment-Annotator web server: rendering and annotating sequence alignments

“…By default, a rapid alignment method is used (12), whereas more accurate and time demanding methods like T-Coffee (4) are available.…”

“…Many of these applications offer their own implementation for server side alignment rendering, e.g. UniProt (1), Pfam (2), SCOPe (3) and T-Coffee (4). This is surprising because software already exists for this task, e.g.…”