msa_diff(1)
Compare two multiple alignments and report differences.
Description
MSA_DIFF
NAME
msa_diff - Compare two multiple alignments and report differences.
DESCRIPTION
Compare two multiple alignments and report differences.
OPTIONS
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--format1, -i FASTA|SS|PHYLIP|MPM|MAF |
Format of first alignment (default is to guess format from file contents).
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--format2, -j FASTA|SS|PHYLIP|MPM|MAF Format of second alignment (default is to guess format from file contents). | |
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--alphabet, -a <alphabet_string> Use given string for alphabet. Can be used to accommodate |
nonstandard characters (e.g., ’b’ for any base or ’ˆ’ for insertion gaps, ’.’ for deletion gaps).
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--ignore-base-id, -b Ignore identity of bases; consider all alphabetical characters equivalent (e.g., A, C, G, T, N, X, b). | |
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--ignore-gap-type, -g |
Ignore type of gap; consider ’-’, ’ˆ’, and ’.’ all equivalent.
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--help, -h Display this help message and exit. |