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T-Coffee specifications
Information
| Unique identifier | OMICS_00989 |
|---|---|
| Name | T-Coffee |
| Alternative names | Tree-based consistency objective function for alignment evaluation, tcoffee |
| Software type | Package/Module |
| Interface | Command line interface |
| Restrictions to use | None |
| Operating system | Unix/Linux |
| Computer skills | Advanced |
| Stability | Stable |
| Maintained | Yes |
Download
Versioning
No version available
Documentation
- Documentation: http://tcoffee.crg.cat/apps/tcoffee/tutorial.html
Additional information
Information
| Unique identifier | OMICS_00989 |
|---|---|
| Name | T-Coffee |
| Alternative names | Tree-based consistency objective function for alignment evaluation, tcoffee |
| Interface | Web user interface |
| Restrictions to use | None |
| Computer skills | Basic |
| Stability | Stable |
| Maintained | Yes |
Documentation
- Documentation: http://tcoffee.crg.cat/apps/tcoffee/tutorial.html
Additional information
Publications for Tree-based consistency objective function for alignment evaluation
Fast and accurate large multiple sequence alignments using root-to-leave regressive computation.
T-Coffee citations
(1034)Selective dissociation between LSD1 and GFI1B by a LSD1 inhibitor NCD38 induces the activation of ERG super enhancer in erythroleukemia cells
[…] sing ECR browser (http://ecrbrowser.dcode.org/). Genomic sequence spanning the ERG locus was obtained from UCSC genome browser (https://genome.ucsc.edu/). DNA sequence alignments were performed using T-coffee server (http://tcoffee.vital-it.ch/apps/tcoffee/do:regular). TF binding sites were analyzed with R-VISTA (http://rvista.dcode.org/). […]
Comparative Genomics Reveals Thousands of Novel Chemosensory Genes and Massive Changes in Chemoreceptor Repertories across Chelicerates
[…] topology for the 11 species. For the analysis, we used OrthoMCL (v2.0.9; ) to identify 1:1 orthologs by clustering the sequences by similarity and then generated an MSA (for each ortholog group) with T-Coffee v11.00 (mcoffe mode; ). After filtering the MSAs with trimAl v1.4 (-automated1 option; ), we estimated the best-fit amino acid substitution model for each MSA with the program jModelTest base […]
Unifying the global phylogeny and environmental distribution of ammonia oxidising archaea based on amoA genes
[…] similarity and different length among proteins, sequences of each subunit were separately aligned with 14 different methods: L-INS-i, E-INS-i and G-INS-i strategies of MAFFT v7; PSI-Coffee, EXPRESSO; T-Coffee; ProbCons v1.12; Probalign v1.3; Prank; Muscle v3.7; MSAProbs v0.9.7; Kalign; Dialign-TX; and Clustal Omega. The 10 best alignments were selected after evaluation with MUMSA based on multiple […]
Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases
[…] To allow a unified mapping of aaRS binding sites, an MSA of 81 (75) representative wild type sequences of Class I (Class II) ( and Files) aaRS was performed. The alignment was calculated with the T-Coffee expresso pipeline [], which guides the alignment by structural information. Using the obtained MSA ( and Files), residues in all aaRS structures were renumbered with the custom script “MSA P […]
The γ33 subunit of R phycoerythrin from Gracilaria chilensis has a typical double linked phycourobilin similar to γ subunit
[…] nucleotide sequences of the γ subunits genes were translated in silico by ExPASy Translate (http://expasy.org). Putative chromophorylation sites were found through a multiple sequence alignment using T-Coffee [] of γ33 subunits from red algae and experimentally determined chromophorylation sites from Gastroclonium coulteri [] and Griffithsia pacifica []. Secondary structure features were calculate […]
Deletion of a Gene Encoding a Putative Peptidoglycan Associated Lipoprotein Prevents Degradation of the Crystalline Region of Cellulose in Cytophaga hutchinsonii
[…] The genome sequence of C. hutchinsonii was obtained from the NCBI database. CLUSTALW was used for the multiple alignment of related Pals. T-COFFEE and MUSCLE were applied to verify the CLUSTALW results. BoxShade was a tool to shade multiple alignment files. […]
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