Simple module to maanage phylogeetic trees. Does not inherit from Annotation.
Working version of neighbour_joining(). Matches phylip for test case.
Created newick() method to derive a newick formatted text string form a tree. Borrows from bioperl.
Documented neighbour_joingin() and added argument to force reconstruction on the sss tree. Not generalized code.
Fixed subtle-but-significant parse error in neighbour_joining().
Fixed randomization procedure in quality2()
Added code to paml() to impose minimum alignment length before dN/dS calculation.
Minor changes to paml() to handle multiple sequences for yn00.
Added -process argument to newick() to return branch lengths as an array.
Minor changes to distance_matrix() to enforce reasonable quality alignments.
 Improvements to quality2() and helper functions -- dS support, fixed ransomizations etc.
Added ability to generate dN and dS matrices to _define_orthogroup(). Some comments.
Minor cleanup and documentation in paml().
Minor changes.