pftools - 3+dfsg-3 main

The pftools package contains all the software necessary to build protein
and DNA generalized profiles and use them to scan and align sequences,
and search databases.
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File formats used by the pftools
* Generalized profiles format and syntax.
* The multiple sequence alignment format (PSA).
* The extended header multiple sequence alignment format (XPSA).
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Programs to build generalized profiles
pfmake
Build a profile from a multiple sequence alignment.
pfscale
Fit parameters of an extreme-value distribution to a profile score list.
pfw
Weight sequences of a multiple sequence alignment to correct for
sampling bias.
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Programs to search with generalized profiles
pfsearch / pfsearchV3
Search a protein or DNA sequence library for sequence segments matching
a profile (V3 is the new version of this tool).
pfscan
Scan a protein or DNA sequence with a profile library
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Conversion programs
psa2msa
Reformat PSA file to Pearson/Fasta multiple sequence alignment file.
ptof
Convert a protein profile into a frame-search profile to search DNA
sequences. To be used with 2ft.
2ft
Converts both strands of DNA into so-called interleaved
frame-translated DNA sequences to search with protein profiles. To be
used with ptof.
6ft
Translates all six reading frames of a double-stranded DNA sequence
into individual protein sequences.
pfgtop
Convert a profile in GCG format into PROSITE format.
pfhtop
Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile.
ptoh
Converts a generalized profile into an approximately equivalent HMM
profile in HMMER1 format (can be read by the hmmconvert program from
the HMMER2 package).