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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Abstract	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.
AbstractList	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.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. 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. 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.
Author	Li, Blaise Lecointre, Guillaume Dettai, Agnès
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Keywords	Missing data Python scripts Phylogeny Reliability Taxonomic congruence Clades
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References	Miyamoto, Fitch (bib7) 1995; 44 Dettai, A., Lecointre, G., 2004. In search of nothothenioid (Teleostei) relatives. Antarctic Science 16 (1), 71–85. Available from Müller, Müller (bib8) 2004; 4 Bininda-Edmonds (bib1) 2003; 52 Edwards, S.V., 2009. Is a new and general theory of molecular systematics emerging? Evolution 63 (1), 1–19. Available from Brinkmann, Van der Giezen, Zhou, Poncelin de Raucourt, Philippe (bib2) 2005; 54 Li, B., Dettai, A., Cruaud, C., Couloux, A., Desoutter-Meniger, M., Lecointre, G., 2009. RNF213, a new nuclear marker for acanthomorph phylogeny. Molecular Phylogenetics and Evolution 50, 345–363. Available from . Li, B., Lecointre, G., 2009. Formalizing reliability in the taxonomic congruence approach. Zoologica Scripta 38 (1), 101–112. Available from
References_xml	– reference: Edwards, S.V., 2009. Is a new and general theory of molecular systematics emerging? Evolution 63 (1), 1–19. Available from: – volume: 44 start-page: 64 year: 1995 end-page: 75 ident: bib7 article-title: Testing species phylogenies and phylogenetic methods with congruence publication-title: Systematic Biology – volume: 52 start-page: 839 year: 2003 end-page: 848 ident: bib1 article-title: Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees publication-title: Systematic Biology – reference: Li, B., Lecointre, G., 2009. Formalizing reliability in the taxonomic congruence approach. Zoologica Scripta 38 (1), 101–112. Available from: – reference: Dettai, A., Lecointre, G., 2004. In search of nothothenioid (Teleostei) relatives. Antarctic Science 16 (1), 71–85. Available from: – volume: 4 start-page: 786 year: 2004 end-page: 788 ident: bib8 article-title: TreeGraph: automated drawing of complex tree figures using an extensible tree description format publication-title: Molecular Ecology Notes – volume: 54 start-page: 743 year: 2005 end-page: 757 ident: bib2 article-title: An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics publication-title: Systematic Biology – reference: Li, B., Dettai, A., Cruaud, C., Couloux, A., Desoutter-Meniger, M., Lecointre, G., 2009. RNF213, a new nuclear marker for acanthomorph phylogeny. Molecular Phylogenetics and Evolution 50, 345–363. Available from: – reference: .
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SubjectTerms	Bayes Theorem Biodiversity Clades Life Sciences Likelihood Functions Missing data Models, Genetic Phylogeny Populations and Evolution Python scripts Reliability Software Taxonomic congruence
Title	rely.py, a python script to detect reliable clades
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