rely.py, a python script to detect reliable clades

rely.py is a program implementing the method to detect independently repeated clades by comparing phylogenies as described in Li and Lecointre (2009) and adapted to incompletely overlapping datasets in Li et al. (2009). The comparison can be performed on trees obtained by any inference method (maxim...

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Vydáno v:Molecular phylogenetics and evolution Ročník 54; číslo 1; s. 306 - 308
Hlavní autoři: Li, Blaise, Dettai, Agnès, Lecointre, Guillaume
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States Elsevier Inc 2010
Elsevier
Témata:
Bayes Theorem
Biodiversity
Clades
Life Sciences
Likelihood Functions
Missing data
Models, Genetic
Phylogeny
Populations and Evolution
Python scripts
Reliability
Software
Taxonomic congruence
Missing data
Python scripts
Phylogeny
Reliability
Taxonomic congruence
Clades
ISSN:1055-7903, 1095-9513, 1095-9513
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Shrnutí:rely.py is a program implementing the method to detect independently repeated clades by comparing phylogenies as described in Li and Lecointre (2009) and adapted to incompletely overlapping datasets in Li et al. (2009). The comparison can be performed on trees obtained by any inference method (maximum parsimony, Bayesian inference, maximum likelihood). The program computes repetition indices, provides greedy summary trees for each validity domain and a nexus matrix representation of the clades weighted by their repetition indices. The additional script concatnexus.py assists the user in preparing the primary analyses, but it can also be used separately to concatenate nexus datasets.
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ISSN:1055-7903
1095-9513
1095-9513
DOI:10.1016/j.ympev.2009.09.034