diff --git a/Makefile b/Makefile
index 7b6592a..63591de 100644
--- a/Makefile
+++ b/Makefile
@@ -6,11 +6,11 @@ WEBDIR = /var/www/hmmer.org/public_html
LABWEB = http://eddylab.org
# Building hmmer.org pages also requires a local git working copy of "labbib", at:
-LABBIB = ~/labbib
+LABBIB = ${HOME}/labbib
# Building hmmer.org pages is coordinated with the lab web pages, in
# this same git repo one level up.
-LABDIR = ../eddylab.org
+LABDIR = ${HOME}/web/eddylab.org
# 'make all' updates the live site.
@@ -34,8 +34,8 @@ test: site/publications-inc.html
site/publications-inc.html: ${LABBIB}/lab.bib ${LABBIB}/master.bib
rm -f site/publications
ln -s ${LABDIR}/site/publications site/publications
- ~/labbib/publications.pl -k 'hmmer' --template=selab.tt --url='${LABWEB}' > site/publications-inc.html
- ~/labbib/publications.pl -k 'hmmer' --template=selab.tt master.bib > site/others-publications-inc.html
+ ~/labbib/publications.pl -n -k 'hmmer' --template=selab.tt > site/publications-inc.html
+ ~/labbib/publications.pl -k 'hmmer' --template=selab.tt master.bib > site/others-publications-inc.html
rm -f site/publications
# Clean up this source directory
diff --git a/site/documentation.html b/site/documentation.html
index d0835ae..79d6452 100644
--- a/site/documentation.html
+++ b/site/documentation.html
@@ -40,8 +40,8 @@ HMMER
Current user guide & release notes
@@ -62,23 +62,13 @@ Briefly, to compile from source:
directory containing precompiled binaries. Installing HMMER takes nothing other
than moving these binaries wherever you want them.
- We believe HMMER compiles and runs on any POSIX-compliant system
+
We believe HMMER compiles and runs on any POSIX-compliant system
with an ANSI C99 compiler, including Mac OS/X, Linux, and any UNIX operating systems.
For more installation and configuration options, see the Installation
chapter of the User Guide (included in the package, and also linked
in the documentation section on this site).
-
-
-
Subversion Access
-
-
Our current development trunk is available via Subversion. To get an anonymous, read-only checkout:
-
svn checkout https://svn.janelia.org/eddylab/eddys/src/hmmer/trunk hmmer
-
-
We welcome code contributions. It's best to give us patches against the development trunk, rather than against the release code (but we'll look at whatever you give us). For developers who've been donating good patches to us for a while, we'll grant write access to the repository.
-
-
@@ -90,11 +80,9 @@
Blog
Papers
- - Eddy SR. Accelerated Profile HMM Searches. PLoS Comput Biol. 2011
- Oct;7(10):e1002195
- - Eddy SR. A Probabilistic Model of Local Sequence Alignment that Simplifies Statistical Significance Estimation. PLoS Comput. Biol. 2008 May 30;4(5):e1000069
- - Eddy SR. A new generation of homology search tools based on probabilistic
- inference. Genome Inform. 2009 Oct;23(1):205-11.
+ - Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 7:e1002195 (2011)
+ - Eddy SR. A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput. Biol. 4:e1000069 (2008)
+ - Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 23:205-11 (2009).
- Other publications about HMMER
@@ -102,7 +90,7 @@
Book
The theory behind profile HMMs:
R. Durbin, S. Eddy, A. Krogh, and G. Mitchison,
-
+
Biological sequence analysis: probabilistic models of proteins
and nucleic acids,
Cambridge University Press, 1998.
@@ -111,27 +99,15 @@
Book
-
-
- A Probabilistic Model of Local Sequence Alignment that Simplifies Statistical Significance Estimation. S. R. Eddy.
- PLoS Comput. Biol.,
- 4:e1000069,
- 2008.
- abstract
-
-
-
-
Support
- HMMER is not intended to be commercial software. In particular, it
- comes with no promise of support whatsoever. We are generally not able
+ Because we're an academic research group, HMMER
+ comes with no promise of support. We are generally not able
to respond individually to requests for help with the package, beyond
- the help already provided in HMMER's documentation. We do respond
- gratefully to useful suggestions for improved documentation, and to
- bug reports.
+ the help already provided in HMMER's documentation. We do appreciate
+ suggestions for better documentation, improvements, and bug reports.
@@ -139,15 +115,18 @@ Support
Reporting bugs
-
Email me
- and please provide as much information as possible so that I can recreate the problem, but equally do not write
- pages and pages. Useful things to include are:
+
Email sean@eddylab.org
+ and please provide me with enough information that I can recreate the problem.
+ Useful things to include are:
- - Input data (or examples, but just sufficient to recreate the problem).
- - Information about the operating system you are using (e.g. % cat /proc/cpuinfo, or % uname -a)
+ - Input data (or examples, a small test case sufficient to recreate the problem).
+ - Information about the operating system you are using (e.g.
cat /proc/cpuinfo or uname -a
+ - Which version of HMMER you're using, and whether you compiled from source or used a binary distro.
-
Without these pieces of information I have to guess or send mails back and forth to determine the cause
- of the issue. Many questions are also covered in the HMMER documentation,
+
Without these pieces of information I have to make guesses and send mails back and forth with you to determine the cause
+ of the issue, and then I get all frustrated and snippy with you because I'm usually pretty busy, and then you think I'm a jerk, and then I feel guilty and bad and have to go away and go running. Nobody wants all that drama.
+
+ Also, many questions are already covered in the HMMER documentation,
so it may be worth browsing there first before sending an e-mail.
diff --git a/site/download.html b/site/download.html
index 34d84da..9873dc9 100644
--- a/site/download.html
+++ b/site/download.html
@@ -44,31 +44,23 @@ The current version is HMMER 3.1b2 (05 Mar
@@ -90,18 +82,14 @@ Windows/Cygwin binaries
| hmmer-3.1b2-cygwin32.tar.gz: |
32-bit |
- [FTP] |
- [HTTP] |
+ [hmmer-3.1b2-cygwin32.tar.gz] |
15MB |
- MD5: 6fe4c2c4eeaebdad9024390195f50059 |
| hmmer-3.1b2-cygwin64.tar.gz: |
64-bit |
- [FTP] |
- [HTTP] |
+ [hmmer-3.1b2-cygwin64.tar.gz] |
16MB |
- MD5: b5e265550be62a395dc475aee158a3f4 |
@@ -132,39 +120,20 @@ Archive of stable representatives of the HMMER1, HMMER2, and HMMER3 lineage
| 3.0 |
March 2010 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: 4cf685f3bc524ba5b5cdaaa070a83588 |
+ [Release Notes] |
+ [hmmer-3.0.tar.gz] |
| 2.3.2 |
Oct 2003 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: 5f073340c0cf761288f961a73821228a |
+ [Release Notes] |
+ [hmmer-2.3.2.tar.gz] |
- | 1.8.5 |
+ 1.8.5 |
Feb 2006 |
-
- | [FTP]
- |
- [HTTP] |
- MD5: b864c2f08a3cc03b7999036457cbe0ba |
+ [Release notes] |
+ [hmmer-1.8.5.tar.gz] |
@@ -176,10 +145,8 @@ Windows binaries
@@ -195,112 +162,50 @@ HMMER3 test releases
| 3.1b1 |
22 Apr 2013 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: e81b689fe1dd7625cff84c08cbead1fc |
+ [Release Notes] |
+ [hmmer-3.1b1.tar.gz] |
| 3.0rc2 |
8 Mar 2010 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: 4a3d8e217556e8ea791d5eaeafb3b072 |
+ [Release Notes] |
+ [hmmer-3.0rc2.tar.gz] |
| 3.0rc1 |
10 Feb 2010 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: f2dbd921c97cf53474abff25ef9cef16 |
+ [Release Notes] |
+ [hmmer-3.0rc1.tar.gz] |
| 3.0b3 |
13 Nov 2009 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: 19c1fddda11c38e5fdfff03d098fa040 |
+ [Release Notes] |
+ [hmmer-3.0b3.tar.gz] |
| 3.0b2 |
21 Jun 2009 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: b8f5f2baa9e56ed029fea9e6939f8d36 |
+ [Release Notes] |
+ [hmmer-3.0b2.tar.gz] |
| 3.0b1 |
17 Jun 2009 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: 67f26fc890e4099b3d695a240990badd |
+ [Release Notes] |
+ [hmmer-3.0b1.tar.gz] |
| 3.0a2 |
12 Mar 2009 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: b829076fc2dc6fe376c1aea2090f16c8 |
+ [Release Notes] |
+ [hmmer-3.0a2.tar.gz] |
| 3.0a1 |
12 Jan 2009 |
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: 73f268e0e8ab8b19a10b3b188f9cb677 |
+ |
+ [hmmer-3.0a1.tar.gz] |
@@ -320,84 +225,38 @@ Other archived versions of HMMER2 and HMMER1
| 2.4i |
Dec 2006 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: dab234c87e026ac1de942450750acd20 |
+ [Release Notes] |
+ [hmmer-2.4i.tar.gz] |
| 2.3.1 |
Jun 2003 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: c724413e5761c630892506698a4716e2 |
+ [Release Notes] |
+ [hmmer-2.3.1.tar.gz] |
| 2.3 |
Apr 2003 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: 09de4dcd66832153412108e36989de48 |
+ [Release Notes] |
+ [hmmer-2.3.tar.gz] |
| 2.2g |
May 2001 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: d7def2007a0aaf2eafb9a96a07986b8c |
+ [Release Notes] |
+ [hmmer-2.2g.tar.gz] |
| 2.1.1 |
Dec 1998 |
-
- [Release Notes]
- |
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: 0f98910a3507b4d52fbe82adc6fa89b5 |
+ [Release Notes] |
+ [hmmer-2.1.1.tar.Z] |
| 1.8.4 |
Jul 1997 |
|
-
- [FTP]
- |
-
- [HTTP]
- |
- MD5: 2c359945f12c69b0c0f0b5a47d370977 |
+ [hmmer-1.8.4.tar.Z] |
diff --git a/site/index.html b/site/index.html
old mode 100644
new mode 100755
index 3f646e0..d660c73
--- a/site/index.html
+++ b/site/index.html
@@ -51,18 +51,27 @@ HMMER: biosequence analysis using profile hidden Markov models
Alternative Download Options
-
HMMER is used for searching sequence databases for homologs of
- protein sequences, and for making protein sequence alignments. It
+
+
HMMER is used for searching sequence databases for sequence homologs,
+ and for making sequence alignments. It
implements methods using probabilistic models called profile hidden
- Markov models (profile HMMs).
+ Markov models (profile HMMs).
+
+
HMMER is often used together with a profile database, such as
+ Pfam or many of the databases
+ that participate in Interpro.
+ But HMMER can also work with query sequences, not just profiles,
+ just like BLAST. For example, you can search a protein query sequence against
+ a database with phmmer, or do an iterative search with
+ jackhmmer.
+
-
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.
-
+
HMMER is designed to detect remote homologs as
+ sensitively as possible, relying on the strength of its
+ underlying probability models. In the past, this strength
+ came at significant computational expense, but as of the new
+ HMMER3 project, HMMER is now essentially as fast as BLAST.
+
HMMER can be downloaded and installed as a command line tool on your own hardware,
and now it is also more widely accessible to the scientific community via
@@ -78,8 +87,8 @@
Perform a Search
News
diff --git a/site/js/main.js b/site/js/main.js
index 654b87a..08dbd0c 100644
--- a/site/js/main.js
+++ b/site/js/main.js
@@ -6,16 +6,16 @@
var link = '/download.html';
if (navigator.userAgent.indexOf("Mac") != -1) {
type = '( MacOSX / Intel )';
- link = 'http://selab.janelia.org/software/hmmer3/3.1b2/hmmer-3.1b2-macosx-intel.tar.gz';
+ link = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-macosx-intel.tar.gz';
}
else if (navigator.userAgent.indexOf("Linux") != -1) {
if (navigator.userAgent.indexOf("x86_64") != -1) {
type = '( Linux / Intel x86_64)';
- link = 'http://selab.janelia.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz';
+ link = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz';
}
else {
type = '( Linux / Intel ia32)';
- link = 'http://selab.janelia.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-ia32.tar.gz';
+ link = 'http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-ia32.tar.gz';
}
}
else if (navigator.userAgent.indexOf("Win") != -1) {
diff --git a/site/publications.html b/site/publications.html
index 9b128b4..bf83ba3 100644
--- a/site/publications.html
+++ b/site/publications.html
@@ -40,7 +40,7 @@
HMMER
-
Publications describing HMMER
+ Publications from the HMMER project