Revision history for Bio::Phylo
0.17
Fixed SVG tree drawing bug on multiple draws
Added to_newick method for node objects
Added set_root_below method for node objects
Added NodeMediator class to manage node relations
Added to_nexus method for taxa objects
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