Binary package “pftools” in ubuntu kinetic

build and search protein and DNA generalized profiles

 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.
 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).
 Programs to build generalized profiles
    Build a profile from a multiple sequence alignment.
    Fit parameters of an extreme-value distribution to a profile score list.
    Weight sequences of a multiple sequence alignment to correct for
    sampling bias.
 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).
    Scan a protein or DNA sequence with a profile library
 Conversion programs
    Reformat PSA file to Pearson/Fasta multiple sequence alignment file.
    Convert a protein profile into a frame-search profile to search DNA
    sequences. To be used with 2ft.
    Converts both strands of DNA into so-called interleaved
    frame-translated DNA sequences to search with protein profiles. To be
    used with ptof.
    Translates all six reading frames of a double-stranded DNA sequence
    into individual protein sequences.
    Convert a profile in GCG format into PROSITE format.
    Convert a HMMER1 ASCII-formatted HMM into an equivalent PROSITE profile.
    Converts a generalized profile into an approximately equivalent HMM
    profile in HMMER1 format (can be read by the hmmconvert program from
    the HMMER2 package).