table of contents|
malform < align_file
will display the final alignment in the file align_file and display these results with a default 60 residues across and to the standard output.
malign file_of_sequences | malform > output_file
the following options to malform are available:
-h a message describing the syntax of the program.
-a normally only the final alignment is printed; to print all intermediate alignments used to construct the final aligment, specify -a.
-i the percentage identities will be computed for the input sequences.
-c plots percent conservation as a segment average; 5 residue segments.
-w# width of alignment; # represents a positive integer.
-m# score alignment according to the matrix specified by the number #. type malform -h for the list of available matrices. the default penalty for gaps is 40.
-p# score alignment and access a gap penalty according to the value of #. the default matrix is the birkbeck matrix (johnson & overington (1993) j.mol.biol, 232, in press). the present matrix is composed from 97 families of aligned 3-d structures (381 structures in total).