ff 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 the next
time seqed is started, you will get a message saying
recovering....can't open
and nothing more will happen. The solution to get seqed working
again is to delete the seqed.log file (by typing 'rm seqed.log').
Note: This problem seems to have been fixed in GCG 9.0
What databases are available for Fasta searches?
The welcome notice when you start up GCG tells you what databases
are available and when each one was last updated.
The databases can be accessed in groups and sub-groups.
For example, Bacterial sequences can be searched separately as
ba:*, gb_ba:*, or as part of Genbank (Genbank:*), or
GenbankPlus (GBPlus:*), or GenEMBLPlus (GEPlus:*). The
database section of the GCG manual
lists the short names for each protein and nucleic acid
database. (On helix, you can also type 'genmanual' and go
to 'Databases').
Genbank and EMBL trade data nightly, so that Genbank encompasses
almost all of EMBL