Display COMPLETE DOCUMENT Scroll Up Scroll DOWN MORE! TOP
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