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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. typically the output from malign(1) is directed to the format program malform(1) which will then display the alignment. 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).
<align_file
>output
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