pegas 1.0-1 has been released. It fixes a bug in plotting haplotype networks.
ape 5.5 has been released. This includes a few new functions, some internal improvements (partitcularly dist.dna
), and several bug fixes. There are two new vignettes on simulation and enumeration of random trees, and on some basic and advanced topics on plotting trees.
pegas 1.0 has been released. The analyses and plotting functionalities of haplotype networks have been improved, including with a new function, mutations
, to show mutations on a plotted network, and a new vignette explaining these improvements; mjn
have also been improved, particularly mjn
which is much faster. The new function write.vcf
object into a VCF file. Several bugs were fixed.
pegas 0.14 has been released. LDscan()
has been improved and a bug was fixed haplotype.DNA()
ape 5.4-1 has been released. This fixes a bug in boot.phylo
introduced in the previous release. rtree
has been improved and can now return trees with all topologies in equal proportions and is more efficient. A bug was also fixed in is.monophyletic
The procedure involved in releasing a new version of ape has improved recently: it is summarized in the Development
ape 5.4 has been released. There are a few new features: the function getAnnotationsGenBank
gets sequence annotations from GenBank and returns them in a friendly format, read.GenBank
gets a few options to make it to more efficient and flexible, seg.sites
is more flexible, and trans
supports more genetic codes. Several bugs were fixed.
pegas 0.13 has been released. It includes an improved haplotype.DNA()
and several bug fixes when handling VCF files.
pegas 0.12 has been released. There are several new functions: F2
to compute population F
to estimate population size from site frequency spectra, theta.tree.hetero
to estimate Θ from heterochronous samples, Rst
to calculate R_st indices with microsatellites, allelicrichness
to analyse allelic richness, as well as several new conversion functions. The summary
objects is now much faster.
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.
ape 5.2 has been released. This includes several new functions: keep.tip
does the opposite operation than drop.tip
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.
pegas 0.11 has been released. The new functions include the generic sw
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.
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
, 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).
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.
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
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).
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
, 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.
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"
performs diagnostics on a DNA alignment; plotBreakLongEdges
help to plot and annotate trees. Several bug were fixed.
pegas 0.9 has been released. It includes the new functions LDscan
for linkage disequilibrium analysis, and na.omit.loci
to drop observations with unclearly identified genotypes. nuc.div
are now generic. Several bugs were fixed in read.vcf
and the analysis of haplotypes is now more efficient.
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
pegas 0.8-2 has been released. This includes mainly bug fixes and a few improvements for the analysis of haplotypes.
pegas 0.8-1 has been released. This is a minor update to adjust with adegenet 2.0.0.
ape 3.3 has been released. It includes three new functions contributed by Tony Ives (binaryPGLMM
, and corphylo
). In addition, rphylo
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).
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".
pegas 0.7 has been released. There are two new functions, geod
, 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.
coalescentMCMC 0.4-1 has been released. This includes a new function for graphical illustration of coalescent simulation.
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.
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
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.
ape 3.1-4 has been released. This fixes a bug from the previous release.
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.
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).
ape 3.1-1 has been released. This corrects a small bug in the previous version.
ape 3.1 has been released. Bipartitions (aka splits) can be manipulated with the new functions (bitsplits
), so that boot.phylo
is now much faster. Two new graphical functions, phydataplot
, help to annotate trees. The function LTT
draws theoretical LTT plots in a very flexible way together with a prediction interval.
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.
coalescentMCMC 0.4 has been released. This is an(other) important update: see the above description of the package.
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.
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.
ape 3.0-11 has been released. This mainly fixes some bugs.
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.
coalescentMCMC 0.2 has been released. The MC code has been completely rewritten. The output is now analysed with the package coda.
ape 3.0-9 has been released. This mainly fixes bugs.
pegas 0.4-5 has been released.
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.
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.
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.
ape 3.0-6 has been released. This includes several important internal changes to make ape faster and more stable.
The first version of coalescentMCMC has been released.
ape 3.0-5 has been released. This includes an improved ace
in cases where SEs cannot be computed.
pegas 0.4-3 has been released. This fixes some internal code.
ape 3.0-4 has been released. This includes an improved read.dna
to read Phylip files, and a more stable and faster bionj
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.
ape 3.0-3 has been released. This fixes a bug in birthdeath
ape 3.0-2 has been released. This fixes a number of bugs and introduces the new function alex
With the publication of the second edition of APER, its page
is under renovation with a list of errata. More soon.
ape 3.0-1 has been released. This notably fixes the bug in read.GenBank
resulting from a change on NCBI
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.gz
See the manual "R Installation and Administration" (sect. 6.3.5).