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AVERAGE-DOT(1) User Contributed Perl Documentation AVERAGE-DOT(1) NAME average-dot.pl SYNOPSIS average-dot.pl [options] --alignment <pp-file> --sequences <pp-file 1> --sequences <pp-file 2>... Options: --help brief help message --man full documentation --verbose be verbose --quiet be quiet --alignment <file> pp file representing the (Lo)Carna alignment --sequences <file> pp files for the input sequences --outfile <file> output file (DEFAULT: averagedot) --threshold <float> for each given threshold (this option can be specified more than once) a copy of the orginal dotplots is created where the dots are highlighted that have in the average plot a probability above the threshold. EXAMPLE The following call ./average-dot.pl -t 0.2 -t 0.5 -t 0.75 -a result.pp -s seq1 -s seq2 -s seq3 creates given a result.pp (as found in the folder "results" of mlocarna) and input pp files seq1 seq2 seq3 (as found in the folder "input" of mlocarna) the following files averagedot_comb_20.pp # average dot plot of the sequences where dots >=0.2 are highlighted averagedot_comb_50.pp # average dot plot of the sequences where dots >=0.5 are highlighted averagedot_comb_75.pp # average dot plot of the sequences where dots >=0.75 are highlighted seq1.pp # dot plot of sequence 1 projected to the alignment with no highlights seq1_comb_20.pp # dot plot of sequence 1 projected to the alignment and dots highlighted # that occur in the average with a probability >=0.2 # in the lower right triangle the average with colored variance info is given seq1_comb_50.pp # ... same as previous for probability >=0.5 seq1_comb_75.pp # ... same as previous for probability >=0.5 + analogous files for seq2 and seq3 All pp files have to be in format "PP 2.0"! DESCRIPTION perl v5.32.1 2022-11-19 AVERAGE-DOT(1)
NAME | SYNOPSIS | EXAMPLE | DESCRIPTION
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