<?xml version="1.0"?>
<tool_dependency>
    <package name="hmmer3_1b1" version="3.1b1">
        <install version="1.0">
            <actions>
                <action type="download_by_url">ftp://selab.janelia.org/pub/software/hmmer3/3.1b1/hmmer-3.1b1.tar.gz</action>
                <action type="autoconf" />
                <action type="change_directory">easel/miniapps/</action>
                <action type="make_install" />
                <action type="set_environment">
                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
                    <environment_variable name="HMMER31_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="C_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
                    <environment_variable name="CPLUS_INCLUDE_PATH" action="prepend_to">$INSTALL_DIR/include</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
HMMER is used for searching sequence databases for homologs of protein
sequences, and for making protein sequence alignments. It implements methods
using probabilistic models called profile hidden Markov models (profile HMMs).

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 mathematical models. In the past, this strength came at significant
computational expense, but in the new HMMER3 project, HMMER is now essentially
as fast as BLAST.

As part of this evolution in the HMMER software, we are committed to making the
software available to as many scientists as possible. Earlier releases of HMMER
were restricted to command line use. To make the software more accessible to
the wide scientific community, we now provide servers that allow sequence
searches to be performed interactively via the Web.

http://hmmer.janelia.org/

        </readme>
    </package>
</tool_dependency>