If you have a multiple sequence alignment in AMPS blockfile format, then you can scan with this using the command:
scanps -btest.blc -a0 > test.scan
The commands and operations are exactly the same as for using a sequence file. Alignments will only show the FIRST sequence from the block file with pre-existing gaps shown as dashes ``-'' rather than spaces `` ''. Note that the length dependent statistics cannot be used with a block file scan.
Alignments in GCG .MSF format or CLUSTAL PIR format can be converted to block file format using the programs ``msf2blc'' and ``clus2blc'' which are distributed with the ALSCRIPT and ASSP program packages. Alternatively, you could generate your alignment using the AMPS package. All these programs are distributed from our ftp server (www.compbio.dundee.ac.uk - please see the README file).