Revision history for Bio::Phylo 0.14 7/Sep/2006 14:23 Removed dependency on XML::Simple 0.13 7/Sep/2006 0:08 Nexus parser now parses interleaved matrices Dependency on Scalar::Util's newness is lessened (i.e. dependency fix, should install easier) Installation choice between MB and EUMM makefiles 0.08 20/Feb/2006 15:14 Improved referential integrity between nodes, taxa, and data. Implemented Fastnexus parser Node object silently implements Bio::Tree::NodeI interface if BioPerl is installed Tree object silently implements Bio::Tree::TreeI interface if BioPerl is installed Added convertor methods for XML and CIPRES Implemented more Matrix methods Implemented symbol tables in Bio::Phylo::Util::CONSTANT Implemented visit method for listable objects Implemented caching infrastructure for calculations Changed object-model to inside-out arrays Added Biodiversity measures code by Aki Mimoto Moved constants and exceptions to Bio::Phylo::Util::* Fixed memory leak due to circular references 0.06, 0.07 Lots of things that I didn't write down 0.05 30/Sep/2005 20:53 Added sequence and alignment objects Added lots more tree methods Unified parsing and unparsing in a single IO module Newick parser now correctly parses multiline strings Implemented exceptions: Bio::Phylo::Exceptions There is a discussion forum: http://www.cpanforum.com/dist/Bio-Phylo Autovivification of blessed hashes now prevented by using 'fields' Implemented a single iterator interface for trees, tree objects, matrices, etc. Implemented a separate treedrawer object for SVG drawings Updated and expanded the documentation 0.04 20/Aug/2005 18:45 Added clone method to duplicate objects Added negative_to_zero method to remove negative branch lengths. 0.03 09/Aug/2005 13:42 Added EXE_FILES switch to Makefile.pl, scripts in bin dir are now installed in the right location. Reorganized Node.pm: "QUERIES" are now grouped under "ACCESSORS" (doesn't change API). Added link to home page: http://www.sfu.ca/~rvosa/ Changed defaults for Svg unparser. Changed parameter setting for unparsers. 0.02 02/Aug/2005 00:28 More example scripts in bin folder Updated documentation for bug reports Changed Newick parser (fewer method calls) Minor bugfixes 0.01 30/Jul/2005 16:25 Initial CPAN release