Man page - msa_diff(1)

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Package:  phast
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• maf_parse(1)
• all_dists(1)
• exoniphy(1)
• base_evolve(1)
• draw_tree(1)
• refeature(1)
• phast(1)
• hmm_train(1)
• msa_view(1)
• stringiphy(1)
• msa_split(1)
• tree_doctor(1)
• convert_coords(1)
• hmm_tweak(1)
• hmm_view(1)
• dless(1)
• msa_diff(1)
• display_rate_matrix(1)
• clean_genes(1)
• prequel(1)
• eval_predictions(1)
Documentations in package:
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Manual

MSA_DIFF

NAME
DESCRIPTION
OPTIONS

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NAME

msa_diff - Compare two multiple alignments and report differences.

DESCRIPTION

Compare two multiple alignments and report differences.

OPTIONS

--format1 , -i FASTA|SS|PHYLIP|MPM|MAF

Format of first alignment (default is to guess format from file contents).

	--format2 , -j FASTA|SS|PHYLIP|MPM|MAF Format of second alignment (default is to guess format from file contents).
	--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).

	--ignore-base-id , -b Ignore identity of bases; consider all alphabetical characters equivalent (e.g., A, C, G, T, N, X, b).
	--ignore-gap-type , -g

Ignore type of gap; consider ’-’, ’ˆ’, and ’.’ all equivalent.

--help , -h Display this help message and exit.

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