SAM 3.2.1 prettyalign - make align2model output more readable R. Hughey & A. Krogh R. Hughey and A. Krogh., SAM: Sequence alignment and modeling software system. Technical Report UCSC-CRL-96-22, University of California, Santa Cruz, CA, September 1996. http://www.cse.ucsc.edu/research/compbio/ismb99.tutorial.html prettyalign prettyalign seqlab prettyalign perl "prettyalign" 0 a2m Alignment perl " $value" 1 readseq_ok_alig perl 1 output_format Output format (-f and -I) "" 2 f i "" i " -I" f " -f" column Output column indices (-c) perl (! $value)? " -c" : "" 1 2 sequence_index Sequence index (number) on each line (-n) perl ($value)? " -n" : "" 0 2 sequence_ID Toggle sequence ID to each line (-i) perl (! $value)? " -i" : "" 1 2 max_inserts Max number of insertions printed (-m) perl (defined $value && $value != $vdef)? " -m $value" : "" 2000000 2 Example: the sequence 'GacguacguG' could be printed out as 'Ga8guG' if 4 was the largest number of insertions that was to be allowed (note that the character 8 is using up one of the positions). By default, insertions of up to length ten thousand are fully printed. If set to zero, no insertions are printed, and no indication of the lack is given. If less than zero, insertion characters are not printed, and that number of digits is used to indicate the length of each insertion. linelength Characters per line (-l) perl (defined $value && $value != $vdef)? " -l $value" : "" 70 2 space_char Char to show inserts (-s) perl ($value && $value ne $vdef)? " -s $value" : "" . 2 max_length Maximum length of input lines (-L) perl (defined $value && $value != $vdef)? " -L $value" : "" 30000 2