<font face="'Times New Roman'" size="3"><span>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. </span></font><div>
<font class="Apple-style-span" face="'Times New Roman'" size="3"><br></font></div><div><font class="Apple-style-span" face="'Times New Roman'" size="3">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. </font></div>
<div><font class="Apple-style-span" face="'Times New Roman'" size="3"><br></font></div><div><font class="Apple-style-span" face="'Times New Roman'" size="3">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:</font></div>
<div><font face="'Times New Roman'" size="3"><span></span></font><font class="Apple-style-span" face="'Times New Roman'" size="3"><a href="http://www.brianomeara.info/tutorials/brownie">http://www.brianomeara.info/tutorials/brownie</a><br>
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Please submit any questions or comments on the use of phyext! Thanks!</div><div><br clear="all"><br>
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