
To add a new species.  Take the last largest .nh tree diagram:

cp 49way.nh 50way.nh

Edit the new 50way.nh tree and insert the organism as
determined from NCBI taxonomy order.  See also, any of:
vertebrates.txt
nematodes.txt
placentals.txt
primates.txt

From that new .nh tree, generate a dissect output

/cluster/bin/phast/tree_doctor --dissect 50way.nh > 50way.dissect.txt

The chainNet.pl script has hard coded numbers in it for the
reference to the proper tree.  Edit that script to update
the reference to the new .nh tree and add the new species to
the new species list.  This will all work as long as the new
species is not next to another new species.

Verify the new chainNet.pl will produce the same numbering
sequence as the previous one did.  To see an order,
check one of the trackDb/organism/trackDb.chainNet.ra files
which have the order for that organism as the top of the tree
