Descriptions have to be explicitely enabled in dumped sequence files
More tests in PantherScore

The Runnable now inherits from RunCommand, which gives natural tools to
test the exit status, the standard error, etc

$ grep STDERR (..)/pantherScore1.03/pantherScore.pl
(..)
print STDERR "Problem with blast on $id\n";
(..)
print STDERR "Missing sequence for $id\n”;
(..)

We've selected these two messages as fatal errors and the runnable will
fail if it finds those strings in the error log
Unusual amino-acids have to be replaced for RAxML
bugfix: parameter for the RAxML phylogenetic model
bugfix: default tree vs input_clusterset_id
"tf_release" is not needed in the default configuration
bugfix: RAxML now needs treebest to root the tree
TreeFam specific parameters
Cleaned-up the default options
Structure for TreeFam-specific analyses
TreeFam needs more memory
 Update EGPairAligner_conf.pm

 bidirectional netting is now the default for Ensembl Genomes, so set it
 to 1.