Dear all,
A new version of ape is in preparation with several significant changes.
The most important ones are:
- All types of phylogenetic trees and networks are now supported:
* trees with singleton nodes are handled with the usual functions
read.tree, plot.tree, ...
* networks are read/write with the new functions read.evonet or
write.evonet (supporting the extended Newick format) and are handled
with several new functions or improvements of previous ones.
- read.tree() and read.nexus() are now based on C code and should be
several times faster.
- The internal code of prop.part() and of reorder.phylo() have been
rewritten in C++ and should be several times faster. This also affects
dist.topo() which is much faster with the default distance.
- The new function Xplor() shows all data files on the local machine in
a Web browser with clickable links to the directories and files.
- image.DNAbin() and image.AAbin() have been improved with several new
options.
All changes are listed in:
http://ape-package.ird.fr/NEWS
A testing version is available as source package and pre-compiled for
Windows; details on how to install them are in:
http://ape-package.ird.fr/ape_installation.html#versions
At this stage, this testing version seems stable. It will be submitted
to CRAN after more tests. We also welcome tests from users and developers.
Best,
Emmanuel & Klaus
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