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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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