NEWS
[2023-03-13] ape 5.8 has been released. It includes several enhancements and bug fixes. See the
NEWS file on
GitHub for details.
[2023-12-13] pegas 1.3 has been released. It has a much faster version of
mst() (1000 times faster with several 100s observations); the code now scales very nearly as O(n^2) in practice. A few bugs have been fixed, and all Web links in the documentation have been updated.
[2023-03-13] ape 5.7-1 has been released. It fixes the implicit dependence on R >= 4.1 introduced in ape 5.7 (the new version should work with R >= 3.4, and certainly with R >= 3.2).
[2023-02-23] pegas 1.2 has been released. It introduces the new function
nullAlleles2NA which changes genotypes with at least one `null allele' into
NA, and fixes a few bugs (VCF files with DOS-style end of lines are now supported).
[2023-02-13] ape 5.7 has been released. The main new feature is the function
muscle5 which calls
MUSCLE5 (
muscle still calls MUSCLE v. 3.1). Besides,
print.LargeNumber gains the options 'latex' and 'digits', and
drop.tip and
keep.tip are now generic functions. Several bugs have been fixed; in particular,
is.binary has been fixed (it now returns FALSE with "((a:1):1,b:2,c:2):1;").
[2022-03-02] ape 5.6-2 has been released. It fixes a few bugs.
[2022-01-07] ape 5.6-1 has been released. It fixes bugs in
axisPhylo() and in
bitsplits().
[2021-12-21] ape 5.6 has been released. There are several new functions:
degree computes the degree of each node in a tree or phylogenetic network,
solveAmbiguousBases replaces R, Y, ... by A, G, C, or T depending on column-wise frequencies.
dnds has been improved and can print details of the calculations. Several bugs were fixed.
[2021-12-16] pegas 1.1 has been released. It fixes a few bugs.
[2021-05-17] pegas 1.0-1 has been released. It fixes a bug in plotting haplotype networks.
[2021-04-25] ape 5.5 has been released. This includes a few new functions, some internal improvements (partitcularly
dist.dna and
nj), 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.
[2021-04-08] 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 and
rmst have also been improved, particularly
mjn which is much faster. The new function
write.vcf writes a
loci
object into a VCF file. Several bugs were fixed.
[2020-09-16] pegas 0.14 has been released.
LDscan() has been improved and a bug was fixed
haplotype.DNA().
[2020-08-13] 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.
[2020-06-24] The procedure involved in releasing a new version of ape has improved recently: it is summarized in the
Development section.
[2020-06-04] 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.
[2019-10-05] pegas 0.13 has been released. It includes an improved
haplotype.DNA() and several bug fixes when handling VCF files.
[2019-10-05] pegas 0.12 has been released. There are several new functions:
F2,
F3 and
F3 to compute population
F-statistics,
stairway 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 and
rarefactionplot to analyse allelic richness, as well as several new conversion functions. The
summary method for
loci
objects is now much faster.
[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 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.gz
See the manual "R Installation and Administration" (sect. 6.3.5).
