[Phyext-commits] Introduction to phyext

[Conrad Stack]

phyext comprises code that was originally part of the RBrownie package.
 It's purpose is to read, write, and manipulate node-annotated phylogenetic
trees in either newick or nexus format.  It is based on the SIMMAP standard
(1.0-1.5) where data is tucked into comments (e.g. [...]) inside of tree
strings.  Mesquite and BEAST use a similar format to export node-annotated
trees.

There are two major reason this code was split off from RBrownie: 1.) It is
easier for me to manage and submit changes and 2.) more people will be able
to use these functions without having to install the C++ prerequisites that
RBrownie calls for.

Some tutorials were written for phyext (when it was still part of RBrownie)
which introduce some or phyext's main read/write/manipulate functions.  They
are on Brian O'Meara's website, under the RBrownie section:
http://www.brianomeara.info/tutorials/brownie

Please submit any questions or comments on the use of phyext!  Thanks!
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