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Sigma, version 1.1.3: simple greedy multiple alignment
Copyright (C) 2006-2009 Rahul Siddharthan <rsidd@imsc.res.in>
Licensed under the GNU General Public License, version 2
Usage: sigma [options] inputfile.fasta [inputfile2.fasta ...]
Each fasta file may contain a single sequence or multiple sequences;
all sequences will be aligned together.
Options:
-A, --aligned_output
(aligned output; this is the default. Compare the -F option.
-A and -F may both be specified, in either order.)
-B, --bgprobfile filename
(name of file containing background probabilities; each line
should contain either a single nucleotide or a dinucleotide
followed by a space and a count. Counts will automatically be
normalised. Trinucleotides and higher will be ignored.)
-b, --bgseqfile filename
(name of auxiliary file from which to read background sequences;
overridden by -B)
-C, --caps_only
(output sequence in uppercase only, as in output of some other
programs like ClustalW and MLagan. Default is mixed-case,
where uppercase indicates aligned sequence, as in Dialign.)
-F, --fasta_output
(multi-fasta output; compare -A option. Default is mixed-case;
for upper-case only, specify -C)
-n, --ncorrel
(background correlation order; 2=dinucleotide is the default,
1=single-site basecounts, 0=0.25 per base. Higher than 2 not
implemented at present.)
-x, --significance
(set limit for how probable the match is by chance: the default
is 0.002, smaller=more stringent)
-h, --help
(display this help summary)
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