bio.info.nih.gov/molbio/molbio_docs/gcg/docs/data_growtree.html">
GrowTree program will not display distance information. However,
the tree generated by GrowTree uses the distances information in the
Distances output file (used as input to the GrowTree program). This
file does have distances information. These values are substitutions
per 100 residues. Remember that GrowTree grows one tree that is
compatible with this information, but it does not grow and evaluate
trees.
If you can calculate the scale from the trees file that
is output by growtree, you may be able to edit the growtree figure
file (which is produced by 'growtree -figure') and manually add the
scale. You can get information about editing the figure file from the
GCG user guide (or type 'genhelp figure'). However, this will be
fairly complicated unless you are very familiar with the figure file
formats.
There are other software packages that will do this including
PAUP for the Mac and
PHYLIP for Mac
and Windows. Phylip may be available on the helix systems in the future;
send mail to the helix staff via the
ptr help system (type 'ptr'
at the helix prompt) if you are interested.
A list of
programs
for Phylogenetic analysis is available from U. Arizona.
I keep getting files called seqed.log in my directory.
If you exit
Seqed abnormally, it creates a seqed.log file to
attempt to rescue work-in-progress. The correct way to exit
seqed is to type Ctrl-D to get to the command line, and then
enter 'exit' (to exit or save) or 'quit' (to exit without saving).
Seqed says 'recovering...' for ever!!
When you exited
Seqed the previous time, something abnormal happened
that caused seqed to rescue your sequence into a file called
seqed.log. If this file was somehow corrupted, then