Analysis of Phylogenetics and Evolution


[+] 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.


[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).

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).

All materials on this page are coyrighted:
© Emmanuel Paradis, 2012 (except IRD logo © IRD and ClusterMaps®)