APE statistics

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Citations per year

Number of citations per year for the bioinformatics software tool APE

Tool usage distribution map

This map represents all the scientific publications referring to APE per scientific context
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Associated diseases

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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 5.2
Stability Stable
methods, stats, parallel, graphics, utils, lattice, tools, nlme, R(≥3.2.0), igraph, expm, gee, Rcpp(≥0.12.0)
Maintained Yes


  • Parafit




No version available


Publications for Analyses of Phylogenetics and Evolution

APE citations


Tracking HIV 1 recombination to resolve its contribution to HIV 1 evolution in natural infection

Nat Commun
PMCID: 5954121
PMID: 29765018
DOI: 10.1038/s41467-018-04217-5

[…] s available for public use on the LANL HIV database (www.hiv.lanl.gov/content/sequence/RAP2017/rap.html). All software is developed in C++, R, and cgi. The R code utilizes functions from the packages ape and seqinr. […]


Do avian blood parasites influence hypoxia physiology in a high elevation environment?

BMC Ecol
PMCID: 5950187
PMID: 29754586
DOI: 10.1186/s12898-018-0171-2

[…] l fit by maximum likelihood (lmekin) within the “coxme” package []. For each model, we controlled for phylogenetic effects by including a phylogenetic correlation matrix as a random effect using the “ape” package []. The phylogenetic correlation matrix was derived from a phylogeny constructed from information by Jetz et al. []. All data was checked for normality and corrected for over-dispersion a […]


Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] tion criterion value was used to estimate phylogenies with 100 bootstrap pseudoreplicates. AMR gene presence was mapped onto the core genome phylogeny using the -phydataplot function in the R package ape (v4.1), with different colours representing different alleles. SRST2-detected AMR genes were queried and visualized against putative plasmid contigs that were assembled with PlasmidSPAdes from sel […]


Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] s groups. We optimized dN/dS on each branch of the gene trees using PAML v. 4.8a [] and calculated the minimum patristic distance based on dS for each sequence in the single-copy gene trees using the ape package [] in R []. We constructed a Beta distribution from the mean and variance of the minimum patristic dS estimates. We removed any sequence that had a nearest neighbor distance in the 99th pe […]


Human local adaptation of the TRPM8 cold receptor along a latitudinal cline

PLoS Genet
PMCID: 5933706
PMID: 29723195
DOI: 10.1371/journal.pgen.1007298

[…] enome-wide average FST between two populations as the “ratio of averages” (equation 10 in []). A neighbor-joining (NJ) tree was calculated using a matrix of the pairwise FST values with the R package ape [], and rooted using ‘mid-point’ rooting with Archaeopteryx []. The full model includes additional predictor variables: latitude and annual mean temperature. In order to achieve convergence of the […]


Chloroplast and nuclear DNA exchanges among Begonia sect. Baryandra species (Begoniaceae) from Palawan Island, Philippines, and descriptions of five new species

PLoS One
PMCID: 5931476
PMID: 29718922
DOI: 10.1371/journal.pone.0194877
call_split See protocol

[…] each parameter was sampled satisfactorily. The first 25% of sampled trees were discarded as burn-in, and the remainder summarized as a maximum clade credibility tree. Trees were visualised using the APE package []. Strict and semi-strict consensus trees combining the two analyses were constructed in PAUP []. […]

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

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