# HG changeset patch
# User jjohnson
# Date 1378386201 14400
# Node ID 3bc37773c6097be13572f9603b8945794963c543

Uploaded

diff -r 000000000000 -r 3bc37773c609 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Sep 05 09:03:21 2013 -0400
@@ -0,0 +1,56 @@
+<?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>