PhyloMAd

PhyloMAd is a software tool for the assessment of phylogenomic model adequateness. The PhyloMAd algorithm uses IQ-TREE for Maximum Likelihood inference, parametric bootstrap simulations and various standard statistical tests. The package includes functions assessing substitution saturation by measuring entropy, phylogenetic tree topology signal strengths, and accuracy of number and clock mode

Topic

Phylogenomics;Phylogenetics;Evolutionary biology;Statistics and probability

Detail

Operation: Phylogenetic tree analysis
Software interface: Library
Language: R
License: GNU General Public License v3
Cost: Free
Version name: -
Credit: The Australian Research Council, McKenzie Fellowship from the University of Melbourne.
Input: -
Output: -
Contact: David A Duchêne david.duchene@sydney.edu.au
Collection: -
Maturity: -

Publications

PhyloMAd: efficient assessment of phylogenomic model adequacy.
Duchêne DA, Duchêne S, Ho SYW (2018). PhyloMAd: efficient assessment of phylogenomic model adequacy. Bioinformatics 34(13): 2300-2301.
https://doi.org/10.1093/bioinformatics/bty103
PMID: 29481585
PMC: -

Download and documentation

Source: https://github.com/duchene/phylomad
Documentation: https://github.com/duchene/phylomad/blob/master/ManualV1.2.pdf
Home page: https://github.com/duchene/phylomad

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