APE home page

PROJECTS

[+] ape

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 over 700 times, and more than 50 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 new package for coalescent analysis; it is still under active development.

NEWS

[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 more and 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).

The SVN repository for ape ?

This is the repository with the last sources of ape. It is regularly updated, so that bug fixes can be followed-up before the next release.

r-sig-phylo ?

This is the "R special interest group on phylogenetic and comparative methods and analyses" mailing list (thanks to the effort of people in NESCent).

EVENTS ?

Courses, workshops, meetings, ... Send me your ads!

April 15–19, 2013: course An introduction to phylogenetics and population genetics with R in Barcelona More.

November 12–16: course Outils d'analyse de la phylogénie et de l'évolution sous R in St Pierre de La Réunion (Cirad).

Analysis of Phylogenetics and Evolution