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<?xml version="1.0"?>
<tool_dependency>
    <package name="hmmer" version="3.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">ftp://selab.janelia.org/pub/software/hmmer3/3.0/hmmer-3.0.tar.gz</action>
                <action type="shell_command">./configure --prefix $INSTALL_DIR</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make check</action>
                <action type="shell_command">make install</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
HMMER is used to search sequence databases for homologs of protein sequences, and to make protein
sequence alignments. HMMER can be used to search sequence databases with single query sequences
but it becomes particularly powerful when the query is an multiple sequence alignment of a sequence family.
HMMER makes a profile of the query that assigns a position-specific scoring system for substitutions,
insertions, and deletions. HMMER profiles are probabilistic models called "profile hidden Markov models"
(profile HMMs) (Krogh et al., 1994; Eddy, 1998; Durbin et al., 1998).

Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older
scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote
homologs, because of the strength of its underlying probability models. In the past, this strength came
at a significant computational cost, with profile HMM implementations running about 100x slower than
comparable BLAST searches. With HMMER3, HMMER is now essentially as fast as BLAST.

The programs in HMMER::

  Single sequence queries: new to HMMER3::

    phmmer Search a sequence against a sequence database. (BLASTP-like)
    jackhmmer Iteratively search a sequence against a sequence database. (PSIBLAST-like)

  Replacements for HMMER2's functionality::

    hmmbuild Build a pro#le HMM from an input multiple alignment.
    hmmsearch Search a pro#le HMM against a sequence database.
    hmmscan Search a sequence against a pro#le HMM database.
    hmmalign Make a multiple alignment of many sequences to a common pro#le HMM.

  Other utilities::

    hmmconvert Convert pro#le formats to/from HMMER3 format.
    hmmemit Generate (sample) sequences from a pro#le HMM.
    hmmfetch Get a pro#le HMM by name or accession from an HMM database.
    hmmpress Format an HMM database into a binary format for hmmscan.
    hmmstat Show summary statistics for each pro#le in an HMM database

ftp://selab.janelia.org/pub/software/hmmer3/3.0/Userguide.pdf
        </readme>
    </package>

</tool_dependency>