APE pipeline

APE specifications


Unique identifier OMICS_12495
Name APE
Alternative name Analyses of Phylogenetics and Evolution
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 5.1
Stability Stable
Source code URL https://cran.r-project.org/src/contrib/ape_5.1.tar.gz
Maintained Yes


  • Parafit



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  • person_outline Emmanuel Paradis <>

Publications for Analyses of Phylogenetics and Evolution

APE IN pipelines

PMCID: 4588643
PMID: 26442762
DOI: 10.1002/ece3.1580

[…] 0.1.1 (posada 2008). the models selected were gtr+i+g for both wsp and 16s rrna genes., the ancestral states of green‐island formation and wolbachia infection were traced using the ace function of “analyses of phylogenetics and evolution” (ape) in r (http://ape-package.ird.fr/) to reconstruct ancestral character states using maximum likelihood and optimized on the moth bayesian topology., […]

PMCID: 4666658
PMID: 26624019
DOI: 10.1371/journal.pone.0143906

[…] through a multiple sequence alignment and a phylogenetic tree, again separated in homologs and orthologs. the alignment and tree is created using the clustalw algorithm, and the r library “ape” (analyses of phylogenetics and evolution) is used to show the phylogenetic tree. these results are only available as a reference sample. the fasta file with the sequences is provided so that the user […]

PMCID: 3305342
PMID: 22438796
DOI: 10.1371/journal.pcbi.1002411

[…] sh3 or kinase interaction, the protein sequences of the gene target and its associated orthologs were aligned using mafft v6.717b [58] with the ‘–auto’ parameter., the r statistical program with the analyses of phylogenetics and evolution (ape) package [59] was used to generate the phylogenetic trees derived from conserved interactions in the sh3 and kinase interaction networks for the 23 yeast […]

APE institution(s)
ISEM, IRD, Univ. Montpellier, CNRS, EPHE, Montpellier, France; Department of Biology, University of Massachusetts Boston, Boston, MA, USA

APE reviews

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