RSS Feed TOMSF
TOMSF converts a multiple sequence alignment produced by one multiple sequence alignment program into the output format of a different multiple sequence alignment program. TOMSF will interconvert among: MSF, CLUSTAL, Phylip, and hmmer formats.
Installed on the Opteron cluster.
Usage:
TOMSF users will find it convenient to use the /biomed/lib/examples/.login.fixed login file. It adds to your default path directories where many sequence analysis packages are stored, sets up the environment for EMBOSS, and defines some environment variables for sequence analysis packages.
tomsf [options] inputfile outputfile
Options:
| -m | output is in MSF format [default] |
| -c | output is in Clustal format |
| -p | output is in Phylip format |
| -h | output is in hmmer format |
| -f | place output to a file [default] |
| -s | place output on stdout |
| -a | easy autoname the output files |
| -g | smart autoname the output files |
| -r | turns off printing of reports |
| -l | all filenames are input filenames (note: this turns on easy autonaming) |