Corrections in test classes.
upated to new java common, ensure backwards compatibility with old clients
Merge branch 'dev' of ssh://git.kbase.us/trees into dev
updated perl port to use a reserved port number
Correction for testing in Jenkins.
Simple multiple sequence alignment type.
added ws tree type
Merge branch 'dev' of ssh://git.kbase.us/trees into dev
updates to spec
First version of MSA (Muscle) was done.
minor updates to spec
Clustal was added as alignment method.
Merge branch 'dev' of ssh://kbase@git.kbase.us/trees into dev
Third party binaries are removed from repo (except FastTree).
T-Coffee was added as supported alignment method.
ProbCons method was added.
Mafft is added as alignment method.
Fix for probcons compilation on linux.
updated tree type, added import from cds stub, added cdmi java clients
Fix for clustalw problem on linux.