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Protocols

T-REX specifications

Information


Unique identifier OMICS_04264
Name T-REX
Alternative name Tree and reticulogram REConstruction
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Vladimir Makarenkov

Publication for Tree and reticulogram REConstruction

T-REX citations

 (54)
library_books

Parallel evolution of Batesian mimicry supergene in two Papilio butterflies, P. polytes and P. memnon

2018
Sci Adv
PMCID: 5906075
PMID: 29675466
DOI: 10.1126/sciadv.aao5416

[…] s were averaged, excluding ortholog groups for which KaKs_Calculator could not calculate the value ( ‘NA’ output) due to lack of informative sites. We constructed a neighbor-joining tree method using T-REX web server (, ), inputting the average Ks data as a distance matrix. […]

library_books

Discovery and Biosynthesis of the Antibiotic Bicyclomycin in Distantly Related Bacterial Classes

2018
Appl Environ Microbiol
PMCID: 5930311
PMID: 29500259
DOI: 10.1128/AEM.02828-17

[…] rt of bcmA to 200 bp downstream of the end of bcmG (average length, 7,224 bp). Phylogenetic analyses were carried out using MUSCLE and RAxML, which were used through the CIPRES science gateway () and T-REX (), and the trees were visualized and edited using iTOL ().The 374 trimmed bcm gene cluster sequences were aligned using MUSCLE () with the following parameters: muscle -in infile.fasta -seqtype […]

library_books

Massive lateral transfer of genes encoding plant cell wall degrading enzymes to the mycoparasitic fungus Trichoderma from its plant associated hosts

2018
PLoS Genet
PMCID: 5908196
PMID: 29630596
DOI: 10.1371/journal.pgen.1007322

[…] ld of 0.9 was applied. To find the most appropriate parameters, we evaluated three different ratios of transfer to GD costs (2, 4 and 6) and compared the predicted gene transfers to those obtained by T-Rex []. The latter infers LGT by quantifying the proximity between two phylogenetic trees using a refinement of the Robinson and Foulds distance using midpoint rooting (see Supporting Information ). […]

library_books

A new fast method for inferring multiple consensus trees using k medoids

2018
BMC Evol Biol
PMCID: 5887197
PMID: 29621975
DOI: 10.1186/s12862-018-1163-8

[…] g to horizontal gene transfers) of clusters of the species tree, the transformed topology of the species tree becomes identical to that of the gene tree. The version of the algorithm available on the T-Rex web site [] was used in our computations.Second, we carried out the version of our k-medoids tree clustering algorithm based on the CH index (Formulas 7 to 11) and the non-squared RF distance to […]

library_books

Geographic population structure in an outcrossing plant invasion after centuries of cultivation and recent founding events

2018
PMCID: 5881623
PMID: 29623183
DOI: 10.1093/aobpla/ply020

[…] st two plants in order to calculate D, so some locations were omitted from this analysis (see for number of samples per location). To visually estimate origins of the US invasion, we used D values in T-REX online () to create a neighbor-joining tree. Bootstrap values for tree branches were created using 1000 repetitions of D in AFLP-SURV and running those with the Consense function in Phylip (). T […]

call_split

Ancient Evolution of Mammarenaviruses: Adaptation via Changes in the L Protein and No Evidence for Host–Virus Codivergence

2018
Genome Biol Evol
PMCID: 5863214
PMID: 29608723
DOI: 10.1093/gbe/evy050
call_split See protocol

[…] of 5 nuclear genes. The phylogeny also included two hosts from different orders (a shrew and a bat). For mammarenavirus phylogenetic reconstruction (RdRp region), we used RAxML through the web server T-REX () using the GTR + G model and a reptarenavirus sequence as the outgroup. Node support was estimated with 1,000 bootstrap replicates and was >90% for all nodes. The tree was manually edited to i […]

Citations

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T-REX institution(s)
Département de sciences biologiques, Université de Montréal, Succ Centre-ville, Montréal, QC; Département d’informatique, Université du Québec à Montréal, Succ Centre-Ville, Montréal, QC, Canada
T-REX funding source(s)
Natural Sciences and Engineering Research Council of Canada [NSERC-249644-2011]; Nature and Technologies Research Funds of Quebec [FQRNT]

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