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ape authors screenshots history faq installation linux unix macintosh windows updating (all oss) stable and testing versions literature documentation citations analysis of phylogenetics and evolution with r development pegas links franais analysis of phylogenetics and evolution projects [+] ape ape is a package written in r for the analysis of phylogenetics and evolution. it is 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 6000 times, and more than 200 r packages depending on ape have been released on cran . to know more about ape, please visit the pages on this site. [+] pegas 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 coalescentmcmc is a 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. [+] phylobench phylobench is a package for phylogenetic benchmarking. it is distributed in github. [+] psmcr psmcr is an r port of psmc, the program for pairwise sequential markovian coalescent (psmc). it is distributed in github. news [2019-03-17] ape 5.3 has been released. the new function dnds computes dn/ds ratios. the namespace files has now explicit exports. see the news file on the right. [2018-09-24] ape 5.2 has been released. this includes several new functions: keep.tip does the opposite operation than drop.tip , rdnabin generates random dna sequences, and updatelabel , a generic function, substitutes labels in a tree or other data sets. several minor bugs were fixed. see the news file on the right. [2018-07-09] pegas 0.11 has been released. the new functions include the generic sw to compute sliding window summaries from dna alignments for each row or averaged among rows, the generic hap.div for haplotype diversity, and dist.asd for the allelic sharing distance for all diploid genotypes (phased or unphased, with two alleles or more). compressed vcf files (.vcf.gz) can now be read remotely. several functions are significantly more efficient, and several bugs were fixed. [2018-04-04] ape 5.1 has been released. the new function write.fasta is much more efficient than write.dna(, format = "fasta") , especially with very long sequences. the new function comparephylo compares two trees with optional plot showing the differences. the functions muscle , clustal , and clustalomega can now perform progressive and tree-guided alignments for both dna and aa sequences. read.fasta can now read amino acid sequence files, and there are new functions to convert from the bioconductor classes to "aabin" . several bugs were fixed (see the news file). [2017-10-31] ape 5.0 has been released. this is a major release. all types of phylogenetic trees and networks are now supported. the new function xplor shows all data files on the local machine in a web browser with clickable links. many functions have been improved and several bugs have been fixed. see more in the news file. [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–death trees 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 b
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