seqalign generate extended alignments for families in a scop families file by using ClustalW with seed alignments.

This is part of Jon Ison's protein structure analysis package. This package is still being developed. Please ignore this program until further details can be documented. All further queries should go to Jon Ison ([email protected]).

Here is a sample session with seqalign:

% seqalign

Mandatory qualifiers:

[-inpath] (string)

Location of scop alignment files (input).

[-extn] (string)

Extension of scop alignment files.

-scopin (infile)

Name of scop hits file (input).

[-outpath] (string)

Location of extended alignment files (Escop format output).

[-outextn] (string)

Extension of extended alignment files.