Man page - pbsdecode(1)

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Package:  phast
apt-get install phast

Manuals in package:
• 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:
• phast

Manual

PBSDECODE

NAME
DESCRIPTION
EXAMPLE
OPTIONS

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NAME

pbsDecode - Decode a binary encoding of a probabilistic biological sequence

DESCRIPTION

Decode a binary encoding of a probabilistic biological sequence (PBS). Outputs a table with a row for each position in the sequence and a column for each base, such that the (i,j)th value is the probability of base j at position i. The same codefile that was used to encode the sequence should be given.

This program performs the inverse function of pbsEncode.

EXAMPLE

Decode an encoded ancestral sequence:

pbsDecode anc.human-mouse.bin mammal.code > anc.human-mouse.probs

where "anc.human-mouse.bin" is a binary encoding of an ancestral sequence produced by pbsEncode or prequel, and "mammal.code" is a codefile produced by pbsTrain.

OPTIONS

--start , -s <sidx>

Decode only the subsequence starting at position <sidx>. Indexing starts with 1.

--end , -e <eidx>

Decode only the subsequence ending at position <eidx>. Indexing starts with 1.

	--discard-gaps , -G Do not report gaps in the PBS.
	--help , -h

Produce this help message.

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