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Triplec specifications

Information


Unique identifier OMICS_33052
Name Triplec
Alternative name Triple consensus
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Arndt von Haeseler
  • person_outline Gregory Ewing

Publication for Triple consensus

Triplec citations

 (6)
call_split

A Rapid and Scalable Method for Multilocus Species Delimitation Using Bayesian Model Comparison and Rooted Triplets

2016
Syst Biol
PMCID: 4997007
PMID: 27055648
DOI: 10.1093/sysbio/syw028
call_split See protocol

[…] 40.In the second simulation, B, delimitation was conducted solely from sets of gene trees (species discovery approach). A consensus tree was built from gene trees from multiple loci using the rooted triple consensus (). Then, the consensus tree was used as the guide tree in the delimitation step. This guide tree contains all possible hierarchical delimitations, from each individual representing a […]

library_books

Genome Based Phylogeny and Comparative Genomic Analysis of Intra Mammary Pathogenic Escherichia coli

2015
PLoS One
PMCID: 4373696
PMID: 25807497
DOI: 10.1371/journal.pone.0119799

[…] r each MCL gene cluster alignment were obtained using maximum likelihood (PhyML v.3.0), and a consensus of these gene trees obtained using the Triple Construction Method as implemented in the program Triplec []. This procedure is based on the observation that the most probable three-taxon tree consistently matches the species tree []. The method searches all input trees for the most frequent of th […]

call_split

An empirical evaluation of two stage species tree inference strategies using a multilocus dataset from North American pines

2014
BMC Evol Biol
PMCID: 4021425
PMID: 24678701
DOI: 10.1186/1471-2148-14-67
call_split See protocol

[…] nce method any method that outputs a species tree estimate. The six species tree inference methods in this study are Concatenation [,], SuperMatrix Rooted Triple (SMRT; []), STEAC [], STAR [], Rooted Triple Consensus (RTC; []), and Minimize Deep Coalescences (MDC; [,]). Concatenation and SMRT are concatenation-based, and STEAC, STAR, RTC, and MDC are consensus methods. Because we have adopted a un […]

library_books

Phylogenomics and the Dynamic Genome Evolution of the Genus Streptococcus

2014
Genome Biol Evol
PMCID: 4007547
PMID: 24625962
DOI: 10.1093/gbe/evu048

[…] ructed from each MCL gene cluster using PhyML v3.0 (). Then, a species tree based on the consensus of the gene trees was constructed using the Triple Construction Method as implemented in the program Triplec (). This procedure is based on the observation that the most probable three-taxon tree consistently matches the species tree (). The method searches all input trees for the most frequent of th […]

library_books

A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree

2012
PMCID: 3637458
PMID: 22546066
DOI: 10.1186/1748-7188-7-7

[…] ts either gene tree topologies or genealogies, i.e., gene trees with branch lengths (coalescence times). Topology-based methods include Minimize Deep Coalescence (MDC) [,], STAR [], STELLS [], rooted triple consensus [] and other consensus and supertree methods [,]. Genealogy-based methods include Bayesian and likelihood methods such as BEST, *BEAST, and STEM [-] and clustering and distance-based […]

call_split

Rooted triple consensus and anomalous gene trees

2008
BMC Evol Biol
PMCID: 2409437
PMID: 18439266
DOI: 10.1186/1471-2148-8-118
call_split See protocol

[…] pology. That is, we only consider if the species tree is recovered correctly or not. The MRe consensus method was implemented and compared to our method with several options.An implementation of root triple consensus program is publicly available at http://www.cibiv.at/software/triplec/ and also [see Additional file ]. […]

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Triplec institution(s)
Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Vienna, Austria
Triplec funding source(s)
Supported by the Austrian Ministry for Science and Research (GEN-AU Bioinformatics Integration Network II) and the WWTF (Vienna Science and Technology Fund).

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