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Protocols

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 citations

 (363)
library_books

Evolutionary novelty in gravity sensing through horizontal gene transfer and high order protein assembly

2018
PLoS Biol
PMCID: 5915273
PMID: 29689046
DOI: 10.1371/journal.pbio.2004920

[…] esis 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 []. […]

library_books

Genome Wide Identification and Expression Profiling of Cytokinin Oxidase/Dehydrogenase (CKX) Genes Reveal Likely Roles in Pod Development and Stress Responses in Oilseed Rape (Brassica napus L.)

2018
Genes
PMCID: 5867889
PMID: 29547590
DOI: 10.3390/genes9030168

[…] ntpellier.fr/phyml/) []. 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 []. […]

library_books

Evolutionary history of Coleoptera revealed by extensive sampling of genes and species

2018
Nat Commun
PMCID: 5768713
PMID: 29335414
DOI: 10.1038/s41467-017-02644-4

[…] calculated 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. […]

call_split

Phylogenomic Perspective on the Relationships and Evolutionary History of the Major Otocephalan Lineages

2018
Sci Rep
PMCID: 5760653
PMID: 29317769
DOI: 10.1038/s41598-017-18432-5
call_split See protocol

[…] ated 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 of each topology […]

library_books

Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage

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

[…] of 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 was as […]

library_books

Microbial eukaryotes have adapted to hypoxia by horizontal acquisitions of a gene involved in rhodoquinone biosynthesis

2018
eLife
PMCID: 5953543
PMID: 29697049
DOI: 10.7554/eLife.34292.028

[…] ndropy package (). Datasets are available at on dryad at DOI: https://doi.org/10.5061/dryad.qp745/4.We tested multiple topologies for the full RquA, Group A and Group B datasets (–) using IQ-TREE and CONSEL. Briefly, maximum likelihood trees for various topologies were generated in IQTREE. Using the ML tree, the constrained trees, and 100 ultrafast bootstrap trees, we computed the site log likelih […]


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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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