CONSEL protocols

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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

 (16)
2017
PMCID: 5453568
PMID: 28570607
DOI: 10.1371/journal.pone.0178657

[…] to assess the probability of the monophyletic relationships between metasterkiella koreana and the genus sterkiella, the approximately unbiased (au) test was performed in consel v. 0.1j [, ]. steps were as described in shazib et al. []. two constrained ml analyses were carried out, i.e., (i) monophyly of m. koreana and sterkiella cavicola, and (ii) monophyly of m. […]

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 () with the approximately unbiased test and the multi-scale bootstrap technique. of the reconfigured trees, 829 (37.6%) were not significantly less likely than the original tree (approximately […]

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

[…] the newick utilities package. 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 0.20 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 […]

2015
PMCID: 4610023
PMID: 26451642
DOI: 10.1186/1471-2105-16-S14-S8

[…] l27-1 and l27-2., treepuzzling: support for the l27 and pdz domains was further evaluated by generating a 95% confidence set of trees based on the expected likelihood weight method as implemented in consel []. tree-puzzle [] was used to sample 50,000 trees, whose likelihoods were assessed using the jtt model with 4 gamma rate categories. a consensus network was constructed from the l27 […]

2015
PMCID: 4632066
PMID: 26384370
DOI: 10.1534/g3.115.020180

[…] v2.75 (http://mesquiteproject.org). the p-values for different tests including approximately unbiased (au) (), kishino-hasegawa (kh) (), and shimodaira-hasegawa (sh) () tests were calculated using consel () to indicate the likelihood of different tree topologies. moreover, geneconv () was also applied to detect possible gene conversion events with default parameters except for 100,000 […]


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CONSEL in publications

 (266)
PMCID: 5915273
PMID: 29689046
DOI: 10.1371/journal.pbio.2004920

[…] testing using the resampling estimated log-likelihood (rell) test, shimodaira–hasegawa (sh) test, kishino–hasegawa (kh) test, and au test was then performed with the paml package ‘codeml’ [] and consel []., the search for fge domain-containing proteins was performed with hmmer3 [], using the fge alignment (pf03781) downloaded from http://pfam.xfam.org. the search was performed on refseq […]

PMCID: 5867889
PMID: 29547590
DOI: 10.3390/genes9030168

[…] []. a bayesian inference tree (bi tree) was generated using the mrbayes program and modelgenerator software []. finally, the optimum topology was chosen using tree-puzzle-5.3 and consel software []. , chromosomal position information for the bnckxs was obtained from the b. napus genome browser, and the genes were mapped onto chromosomal linkage groups with mapchart []. […]

PMCID: 5768713
PMID: 29335414
DOI: 10.1038/s41467-017-02644-4

[…] with raxml using the -f g option. then, the site log-likelihood file was used as input to estimate the p-values for each alternative hypothesis using the au test implemented in the program consel., divergence times were estimated by using mcmctree in the paml package with the uncorrelated rate model (clock = 2). the protein raxml tree was used as the reference topology. twenty fossils […]

PMCID: 5760653
PMID: 29317769
DOI: 10.1038/s41598-017-18432-5

[…] dataset. we implemented ml analyses for the four datasets with raxml 7.2.6 under the best fit model for 500 and 1,000 bootstrap replicates. to evaluate the confidence of all topology hypotheses, consel was used to implement the au test, the shimodaira-hasegawa (wsh) test, the kishino-hasegawa (kh) test and the bootstrap probability (bp) test after the per site log-likelihoods […]

PMCID: 5897096
PMID: 29648535
DOI: 10.7554/eLife.33034.033

[…] saccharomycotina as the constrained topology ( and ). the best tree was inferred in raxml, and ml values for constrained and unconstrained trees were also calculated. the au test () implemented in consel () 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 clade and c. infanticola […]


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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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