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CONSEL computational protocol

CONSEL specifications

Information


Unique identifier OMICS_24620
Name CONSEL
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Stability Stable
Maintained No

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Publication for CONSEL

CONSEL IN pipelines

 (13)
2018
PMCID: 5897096
PMID: 29648535
DOI: 10.7554/eLife.33034.033

[…] 1a and figure 5—figure supplement 1c). the best tree was inferred in raxml, and ml values for constrained and unconstrained trees were also calculated. the au test (shimodaira, 2002) implemented in consel (shimodaira and hasegawa, 2001) was used to compare the unconstrained best tree and the best tree given a constrained topology. to test the independence of adh1 acquisition, monophily of w/s […]

2016
PMCID: 5183456
PMID: 27648812
DOI: 10.1038/ismej.2016.116

[…] monophyly of recipient genes, and when these were paraphyletic (2205 trees, 17.48%), we tested for the likelihood of an alternative tree with recipients consolidated into one clade. for this we used consel (shimodaira and hasegawa, 2001) with the approximately unbiased test and the multi-scale bootstrap technique. of the reconfigured trees, 829 (37.6%) were not significantly less likely […]

2015
PMCID: 4415804
PMID: 25928886
DOI: 10.1371/journal.pone.0125043

[…] mtdna (nd2 dataset) and the multilocus (aflp) nc dataset were evaluated for significant differences between cyto-nuclear discordant topologies with approximately unbiased (au) tests [68] using consel v. 0.1 [69]., our experimental het design of the aflp dataset contained consecutive full and partial taxon removal experiments of every single individual (n = 93; except for the outgroup […]

2015
PMCID: 4444528
PMID: 25945739
DOI: 10.1038/nature14447

[…] the newick utilities package68. for each alignment tested, per-site maximum likelihood was calculated for both hypothesis trees with raxml 8.0.9, using the option ‘–f g’, and the protgammalg model. consel 0.2081 was then used to perform approximately unbiased tests, using default settings., a reference set of 59 highly conserved, low- or single-copy genes were used both as taxonomic markers […]

2014
PMCID: 4261875
PMID: 25091111
DOI: 10.1186/1742-4690-11-61

[…] by prottest 2.4 [84] under the aic criterion, was used (pol: rtrev + γ(4) + f; env: wag + γ(4) + f). a molecular clock was not imposed, and ambiguous sites were included. au tests were performed in consel [88] with default settings., additional bayesian fv phylogenies were constructed using the same settings as described above. one included a number of short fragments of other lorisiforme fv […]

CONSEL institution(s)
The Institute of Statistical Mathematics, Minatoku, Tokyo, Japan
CONSEL funding source(s)
Supported by Grant-in-Aids from JSPS (12780179, 12554037), and from MEXT (11NP0201).

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