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Protocols

TRIBE-MCL specifications

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Unique identifier OMICS_19420
Name TRIBE-MCL

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Publication for TRIBE-MCL

TRIBE-MCL citations

 (59)
library_books

Comparative Transcriptomics Among Four White Pine Species

2018
PMCID: 5940140
PMID: 29559535
DOI: 10.1534/g3.118.200257

[…] The Markov Cluster Algorithm (MCL) was implemented via TRIBE-MCL to identify shared and unique gene families among the white pine species analyzed (). All translated sequences were filtered for a minimum length of 100aa. An all-vs.-all BLASTP search was p […]

library_books

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

2017
Nat Commun
PMCID: 5711932
PMID: 29196618
DOI: 10.1038/s41467-017-01491-7

[…] The protein sequences used for ortholog analysis (see “Construction of orthologous groups”) were also clustered into tribes using TRIBE-MCL, with a BLASTp E-value cutoff of 1e-5 and an inflation value of 5.0. Phylogenetic analysis of the protein tribes is described in Supplementary Method . […]

library_books

A dual strategy expression screen for candidate connectivity labels in the developing thalamus

2017
PLoS One
PMCID: 5448750
PMID: 28558017
DOI: 10.1371/journal.pone.0177977

[…] searches to annotate the predicted proteomes of worm, fly, mouse and human. We also generated a matrix of pairwise BLAST scores across all the members of these proteomes and clustered them using the TRIBE-MCL algorithm, as previously described []. We screened through the resultant outputs to find clusters with mammalian and fly or worm members encoding predicted transmembrane proteins, which also […]

library_books

Genomics insights into different cellobiose hydrolysis activities in two Trichoderma hamatum strains

2017
Microb Cell Fact
PMCID: 5395790
PMID: 28420406
DOI: 10.1186/s12934-017-0680-2

[…] n from YYH13 was kept. Finally, the mean PID and standard deviation were calculated based on the revised one-to-one relationships for each pair of genome.Genome difference genes were identified using Tribe-MCL (inflation value = 1.6) [] with the original gene set. Each genome difference genes were examined using genBlastG. For each genome difference gene, genBlastG was used against the two other g […]

library_books

Deciphering the distance to antibiotic resistance for the pneumococcus using genome sequencing data

2017
Sci Rep
PMCID: 5311915
PMID: 28205635
DOI: 10.1038/srep42808

[…] score ratio’ (LS-BSR) pipeline allowing 10% amino acid difference within clusters. The resulting representative sequences per group (“centroids”) were clustered through a Markov Clustering Algorithm (TRIBE-MCL) with an inflation factor of 2.5, resulting into 4687 orthologous groups (OGs). For each OG, we generated a binary metric of the presence (1) or absence (0) of a representative coding sequen […]

library_books

Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana)

2016
PMCID: 5144951
PMID: 27799338
DOI: 10.1534/g3.116.032805

[…] The Markov cluster (MCL) algorithm analysis (v.12-068) (), as implemented in TRIBE-MCL (), was used to cluster the 385,329 protein sequences from 13 species into orthologous groups. Species included: Glycine max (37,388), Ricinus communis (28,113), Populus trichocarpa (36,393) […]


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TRIBE-MCL institution(s)
Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, UK; Centrum voor Wiskunde en Informatica, Amsterdam, Netherlands

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