Analysis of Phylogenetics and Evolution
ape is a package written in R for the analysis of phylogenetics and evolution. It is reasonably used within the community of evolutionary biologists for data analysis and as a framework for the development of new analytical methods. Since 2003, ape has been cited more than 5000 times, and more than 200 R packages depending on ape have been released on CRAN.
pegas is a package for the analysis of population and evolutionary genetics; it is a companion package of ape. To know more about pegas, please visit its page on this site.
coalescentMCMC is a new package for coalescent analysis. Since version 0.4, this package has been considerably improved. Several models of temporal change of Θ are available and can be compared with log-likelihood or information criteria (AIC, BIC, DIC). Running the chains is very flexible so that they can be run successively, in parallel, or in interaction. The outputs are analysed with the package coda. So all analyses (data preparation, running the chains, convergence diagnostics, parameter estimation, model comparison, …) are done in the same environment! Computing times are reasonably short. The package comes with two vignettes giving details on how to run these analyses.
[2017-05-03] pegas 0.10 has been released with several new functions to construct and plot haplotype networks: msn for the minimum spanning network, rmst for the randomised minimim spanning tree, mjn for the median-joining network (using binary or DNA data), and plotNetMDS for a new way to plot networks in 2- or 3-D. The display of mutations on network links has been improved with the new default being small segments. There is also a new all.equal.haploNet method to compare networks, a new haplotype.character method to get haplotypes from any kind of genotypic data, and a general purpose dist.hamming function.
[2017-02-15] ape 4.1 has been released. This includes two new functions: read.fastq to read FASTQ files and Xplorefiles to find files. There are few bug fixes (detailed in the NEWS file).
[2016-12-01] ape 4.0 has been released. This new version includes quite a lot of new features (see NEWS file on the right). DNA sequences objects can now be longer than 2.1 billion bases: the limit is 4.5 Pb. Bootstrap analyses can be parallelized on multi-cores. read.GenBank is faster and can now read contigs and scaffolds. There are several new functions such as estimate.mu and estimate.dates, contributed by Bradley Jones, to estimate the mutation rate and the dates for a rooted phylogenetic tree with dated tips. See more in the NEWS file.
[2016-05-24] ape 3.5 has been released. It includes eleven new functions to work with the new class "AAbin" storing amino acid sequences, including trans for translation of DNA sequences and complement to return the complement of a "DNAbin" object. checkAlignment performs diagnostics on a DNA alignment; plotBreakLongEdges and drawSupportOnEdges help to plot and annotate trees. Several bug were fixed.
[2016-04-15] pegas 0.9 has been released. It includes the new functions LDscan and LDmap for linkage disequilibrium analysis, and na.omit.loci to drop observations with unclearly identified genotypes. nuc.div and theta.s are now generic. Several bugs were fixed in read.vcf and the analysis of haplotypes is now more efficient.
[2015-05-29] ape 3.4 has been released. It includes seven new functions, new styles for phydataplot (including for plotting alignments with tree), and plot.phylo has a new option (align.tip.label) to align the labels of the tips when the tree is not ultrametric (see the new examples in ?phydataplot).
[2015-09-25] pegas 0.8-2 has been released. This includes mainly bug fixes and a few improvements for the analysis of haplotypes.
[2015-06-24] pegas 0.8-1 has been released. This is a minor update to adjust with adegenet 2.0.0.
[2015-05-29] ape 3.3 has been released. It includes three new functions contributed by Tony Ives (binaryPGLMM, binaryPGLMM.sim, and corphylo). In addition, rphylo simulates
birth–deathtrees under any time-dependent model of diversification, and del.colgapsonly removes the columns of a DNA alignment that contain only gaps (useful when a matrix is extracted from a large alignment). As usual, there are several improvements and bug fixes (see NEWS).
[2015-05-20] pegas 0.8 has been released. There are several new functions for the analysis of VCF files (see ?VCFloci), and read.vcf has been improved and can now read 100,000's loci in a few seconds. There is a subset method for haplotypes (with respect to their frequencies and/or proportion of missing data). The new function alleles2loci transforms a matrix of alleles into an object of class "loci".
[2015-03-05] pegas 0.7 has been released. There are two new functions, geod and geoTrans, for analysis of geographic data. The analysis of haplotypes from DNA sequences has been improved: haploNet now returns alternative links, and there is a new function, replot, to help plot networks.
[2015-03-03] coalescentMCMC 0.4-1 has been released. This includes a new function for graphical illustration of coalescent simulation.
[2014-12-05] ape 3.2 has been released. It includes several new functions: reconstruct contributed by Manuela Royer-Carenzi and Gilles Didier with new algorithms for ASR; vcv2phylo contributed by Simon Blomberg transforms a VCV matrix into a tree; nodepath finds paths of nodes in a tree; def helps to (re)define attributes for annotating trees; several as.DNAbin methods convert DNA sequence sets from BioConductor. See the NEWS file for bug fixes and other changes.
[2014-08-21] pegas 0.6 has been released. Phased genotypes can now be read and analysed. Some new functions include: read.vcf reads VCF files; haplotype is now generic with methods for "DNAbin" and "loci" objects; LD and LD2 test for linkage disequilibrium with phased and unphased genotypes, respectively; and proba.genotype computes expected genotype probabilities under Hardy–Weinberg equilibrium for all levels of ploidy and any number of alleles.
[2014-07-15] ape 3.1-4 has been released. This fixes a bug from the previous release.
[2014-07-12] ape 3.1-3 has been released. It includes a new function (rtt) contributed by Rosemary McClosekey to root trees with non-contemporaneous sequences. Among the few bugs fixes: FASTA files can be read through Internet (this was possible with older versions of ape but not supported with the recent ones), and reading old GenBank records (i.e., before 1990) should not give error anymore.
[2014-05-27] ape 3.1-2 has been released. This mainly corrects a few bugs. Plotting of circular trees has been made more flexible. Ancestral state reconctruction of discrete characters is now done with joint estimation by ace (marginal reconstruction is still possible).
[2014-03-07] ape 3.1-1 has been released. This corrects a small bug in the previous version.
[2014-03-04] ape 3.1 has been released. Bipartitions (aka splits) can be manipulated with the new functions (bitsplits and countBipartitions), so that boot.phylo is now much faster. Two new graphical functions, phydataplot and ring, help to annotate trees. The function LTT draws theoretical LTT plots in a very flexible way together with a prediction interval.
[2014-01-10] pegas 0.5-1 has been released. The function MMD has been improved: it displays the expected distribution of mismatches under the assumption of constant population.
[2013-12-04] coalescentMCMC 0.4 has been released. This is an(other) important update: see the above description of the package.
[2013-10-27] coalescentMCMC 0.3 has been released. This is an important update: the MCMC algorithm has been carefully checked and is much faster. It is now possible to fit a time-dependent coalescent model. The vignette has been updated with a (almost) complete analysis.
[2013-10-08] pegas 0.5 has been released. Plot of haplotype networks has been improved (see the new function haploFreq). The new function theta.msat calculates THETA using micro-satellites.
[2013-10-01] ape 3.0-11 has been released. This mainly fixes some bugs.
[2013-09-10] ape 3.0-10 has been released. This includes important internal recoding. The new function rotateConstr rotates internal branches given a constraint on the order of the tips. The long-lasting bug plot(phy, main = "A title...") has been fixed.
[2013-07-19] coalescentMCMC 0.2 has been released. The MC code has been completely rewritten. The output is now analysed with the package coda.
[2013-07-19] ape 3.0-9 has been released. This mainly fixes bugs.
[2013-06-06] pegas 0.4-5 has been released.
[2013-04-02] ape 3.0-8 has been released. This includes the new function ewLasso testing whether an incomplete distance matrix uniquely determines the edge weights of an unrooted topology. Some bugs in read.dna(, "fasta") have been fixed.
[2013-01-23] pegas 0.4-4 has been released. This includes a new code for minimum spanning tree, a new estimator of THETA, and some bug fixes.
[2013-01-21] ape 3.0-7 has been released. This includes a new function for molecular dating by PL and ML (chronos). Plotting circular trees has also been improved. Reading FASTA files is much faster and more efficient.
[2012-10-20] ape 3.0-6 has been released. This includes several important internal changes to make ape faster and more stable.
[2012-10-08] The first version of coalescentMCMC has been released.
[2012-08-01] ape 3.0-5 has been released. This includes an improved ace in cases where SEs cannot be computed.
[2012-07-31] pegas 0.4-3 has been released. This fixes some internal code.
[2012-06-13] ape 3.0-4 has been released. This includes an improved read.dna to read Phylip files, and a more stable and faster bionj.
[2012-04-24] pegas 0.4-2 has been released. This fixes a bug in amova where the P-value of the highest level was not correctly computed.
[2012-04-24] ape 3.0-3 has been released. This fixes a bug in birthdeath.
[2012-04-05] ape 3.0-2 has been released. This fixes a number of bugs and introduces the new function alex (alignment explorator).
[2012-03-15] With the publication of the second edition of APER, its page is under renovation with a list of errata. More soon.
[2012-02-17] ape 3.0-1 has been released. This notably fixes the bug in read.GenBank resulting from a change on NCBI.
[2012-02-01] Since the release of R 2.14.0, I recommend to install ape with "byte-compile" for a substantial increase in performance. This is not the default; for instance under Linux:
R CMD INSTALL --byte-compile ape_3.0-2.tar.gzSee the manual "R Installation and Administration" (sect. 6.3.5).
ape souce code
For the last sources, see on this site:
Menu Installation -> Stable and Testing Versions.
A list of all the new features (since version 0.1) regularly updated with the on-going developments.
This is the "R special interest group on phylogenetic and comparative methods and analyses" mailing list (thanks to the effort of people in NESCent).
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Introduction to phylogenetic analysis with RMore.
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