Commit 0d174cd3 authored by Andreas Tille's avatar Andreas Tille

Imported Upstream version 1.1.1

parent 4c587125

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.

Infernal - inference of RNA secondary structure alignments
http://infernal.janelia.org/
----------------------------------------------------------------
:: About this software:
Infernal is an implementation of "covariance models" (CMs), which
are statistical models of RNA secondary structure and sequence
consensus.
You give Infernal a multiple sequence alignment of a conserved
structural RNA family, annotated with the consensus secondary
structure. The "cmbuild" program builds a statistical profile of
your alignment. That CM can be used as a query in a database
search to find more homologs of your RNAs (the "cmsearch"
program). You can also use a CM of a representative alignment of
your sequence family to create a larger consensus alignment of
any number of RNAs.
We still consider this software to be under development. Our
research efforts are focused on reducing the computatational
complexity of CM algorithms so searches are faster. We haven't
yet spent as much effort as we'd like on making Infernal pretty
and user-friendly. Nonetheless, Infernal provides the software
engines behind the Rfam RNA database (http://rfam.janelia.org).
:: Getting Infernal:
WWW: http://infernal.janelia.org/
Distro tarballs: ftp://selab.janelia.org/pub/software/infernal/
:: Developer access (password required):
SVN: https://svn.janelia.org/eddylab/eddys/src/infernal
:: Installation:
See the Userguide.pdf for complete instructions. In brief:
% ./configure
% make
The programs will be in the src/ subdirectory.
Additionally, 'make check' will run an automated test suite, and
'make install' will install the programs in /usr/local/bin by
default.
:: Getting started:
For documentation, including installation instructions and a
tutorial, see the Infernal User's Guide: Userguide.pdf.
:: Reference:
- EP Nawrocki, DL Kolbe, and SR Eddy, "Infernal 1.0: inference of
RNA alignments" Bioinformatics 25:1335-1337 (2009).
:: Other references:
- DL Kolbe and SR Eddy, "Local RNA structure alignment with
incomplete sequence", Bioinformatics 25:1236-1243 (2009).
- EP Nawrocki and SR Eddy, "Query-dependent banding (QDB) for
faster RNA similarity searches", PLoS Computational Biology,
3:e56 (2007).
- SR Eddy, "A memory efficient dynamic programming algorithm for
optimal structural alignment of a sequence to an RNA secondary
structure", BMC Bioinformatics, 3:18 (2002).
- R Durbin, S Eddy, A Krogh, G Mitchison. Biological Sequence
Analysis: Probabilistic Models of Proteins and Nucleic Acids.
Cambridge University Press, Cambridge UK. (1998).
- S.R. Eddy and R. Durbin, "RNA sequence analysis using
covariance models", Nucl. Acids Res. 22:2079-2088 (1994).
:: Credits:
The current Infernal developer team at HHMI Janelia Farm:
Diana Kolbe, Eric Nawrocki, and Sean Eddy.
Configuring Infernal for MPI parallelization.
---------------------------------------------
If you have an MPI-compliant library installed (LAM, MPICH, OpenMPI)
and you want to use MPI parallelization, enable MPI with the
--enable-mpi flag to the configure script:
% ./configure --enable-mpi
% make
This will build the normal seven Infernal executables and four of
these executables (cmalign, cmcalibrate, cmscore and cmsearch) will be
MPI programs that can either be run in serial mode or in MPI mode by
using the --mpi option and running with an MPI-compliant library.
Notes on running cmsearch in MPI mode on a cluster
--------------------------------------------------
The following is an example from our configuration. We use LAM MPI, on
a cluster that uses the Sun Grid Engine (SGE) as its queueing manager.
Your mileage may vary: you may need to consult your local MPI or
cluster guru if you're running a different MPI package or a different
queue manager.
Make sure 'cmsearch' is in your $PATH.
To run the CM foo.cm against the database genome.fa on 100 CPUs
execute the following on the head node (login-eddy.int.janelia.org):
$ qsub -N foo -o foo.out -b y -cwd -V -j y -pe lam-mpi-tight 100 'mpirun C cmsearch --mpi -E 50 foo.cm genome.fa > cmsearch.out'
This submits a single SGE job named 'foo' to the cluster. This job
will run cmsearch in parallel mode on 100 processors and report all
hits with E-values below 50 to cmsearch.out.
Infernal - inference of RNA secondary structural alignments
Copyright (C) 2014 Howard Hughes Medical Institute.
------------------------------------------------------------------
Copyright (C) 2009 HHMI Janelia Farm Research Campus
Copyright (C) 2013 HHMI Janelia Farm Research Campus
Portions Copyright (C) 1991-2009 Sean R. Eddy
Portions Copyright (C) 2005-2009 Eric P. Nawrocki
Portions Copyright (C) 2005-2009 Diana L. Kolbe
Portions Copyright (C) 1991-2013 Sean R. Eddy
Portions Copyright (C) 2005-2013 Eric P. Nawrocki
Portions Copyright (C) 2005-2011 Diana L. Kolbe
Portions Copyright (C) 2004 Zasha Weinberg
Portions Copyright (C) 1990 Don G. Gilbert
Portions Copyright (C) 1995-2006 Washington University in St. Louis
......@@ -14,10 +16,15 @@ Copyright (C) 2009 HHMI Janelia Farm Research Campus
Portions Copyright (C) 1989-2001 Free Software Foundation
Portions Copyright (C) 1991 Massachusetts Institute of Technology
Infernal includes the HMMER software package, which has its own license and
copyright information. See hmmer/COPYRIGHT and hmmer/LICENSE.
Infernal uses the Easel software library, which has its own license and
copyright information. See easel/COPYRIGHT and easel/LICENSE.
Infernal is distributed under the terms of the GNU General Public
License version 3 (GPLv3). See the file LICENSE for details.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or (at
......@@ -31,5 +38,9 @@ GNU General Public License for more details.
A copy of the GNU General Public License is in the file LICENSE. You
may also obtain a copy from <http://www.gnu.org/licenses/>.
------------------------------------------------------------------
The Infernal development team
HHMI Janelia Farm Research Campus
http://infernal.janelia.org/
Brief installation instructions
Infernal 1.1.1; July 2014
-------------------------------------------------------------
These are quick installation instructions. For complete documentation,
including customization and troubleshooting, please see the
Installation chapter in the Infernal User's Guide (Userguide.pdf).
Starting from a source distribution, infernal-1.1.1.tar.gz:
uncompress: uncompress infernal-1.1.1.tar.gz
unpack: tar xf infernal-1.1.1.tar
move into new directory: cd infernal-1.1.1
configure: ./configure
build: make
automated tests: make check
automated install: make install
Infernal is designed to run on POSIX-compatible platforms, including
UNIX, Linux and MacOS/X. The POSIX standard essentially includes all
operating systems except Microsoft Windows. We have tested most
extensively on Linux and on MacOS/X, because these are the machines we
develop on.
Infernal depends on vector parallelization methods that are supported
on most modern processors. Infernal requires either an x86-compatible
(IA32, IA64, or Intel64) processor that supports the SSE2 vector
instruction set, or a PowerPC processor that supports the Altivec/VMX
instruction set. If your platform does not support one of these vector
instruction sets, you won’t be able to install and run Infernal 1.1 on
it.
-------------------------------------------------------------
Starting from a Subversion (SVN) working copy:
If you have checked Infernal out from its Subversion repository, there's
some additional stuff you need to do one-time-only in your new working
directory:
ln -s easel/aclocal.m4 aclocal.m4
ln -s easel/aclocal.m4 hmmer/aclocal.m4
autoconf
(cd easel; autoconf; cd ../hmmer; autoconf;)
-------------------------------------------------------------
The Infernal development team
HHMI Janelia Farm Research Campus
http://infernal.janelia.org/
......@@ -672,3 +672,4 @@ may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<http://www.gnu.org/philosophy/why-not-lgpl.html>.
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Infernal - inference of RNA secondary structure alignments
http://infernal.janelia.org/
Version 1.1.1; July 2014
Copyright (C) 2014 Howard Hughes Medical Institute.
------------------------------------------------------------------
Infernal is an implementation of covariance models (CMs), which are
statistical models of RNA secondary structure and sequence consensus.
You give Infernal a multiple sequence alignment of a conserved
structural RNA family, annotated with the consensus secondary
structure. The "cmbuild" program builds a statistical profile of your
alignment. That CM can be used as a query in a database search to find
more homologs of your RNAs (the "cmsearch" program). You can also use
a CM of a representative alignment of your sequence family to create a
larger consensus alignment of any number of RNAs (the "cmalign"
program). Infernal is the software engine underlying the Rfam RNA
database (http://rfam.janelia.org).
Other files to read in the top-level source directory:
INSTALL Brief installation instructions.
Userguide.pdf The Infernal User's Guide.
COPYRIGHT Copyright and license information.
LICENSE The GNU General Public License (GPLv3).
To get started after installation, see the Tutorial section in the
Infernal User's Guide (Userguide.pdf).
-------------------------------------------------------------------
The Infernal development team
HHMI Janelia Farm Research Campus
http://infernal.janelia.org/
Infernal 1.1.1 release notes
http://infernal.janelia.org/
EPN, Mon Jul 21 14:01:18 2014
________________________________________________________________
Infernal 1.1.1 is the first update release for Infernal 1.1.
Notable changes from 1.1:
- In cmsearch and cmscan, the maximum size of an HMM banded matrix is
now model size dependent instead of the fixed 128 Mb maximum size
previously used. The maximum size ranges from 128 Mb (for normal
size and small models) to 512 Mb (for large models). This change
will only rarely and subtly affect search and alignment results for
large models (window size 'W' parameter > 1000, e.g. SSU and LSU
rRNA models) and will not affect results at all for the vast
majority of models.
- Fixed bug #i41, which caused a failure with binary output of
in the 'cmconvert' program.
- Fixed bug #i42, which affected alignments for truncated hits
in rare cases by using slightly tighter HMM band constraints than
necessary.
- Fixed bug #i43, which caused cmsearch to fail with an error message
for large models (> 3000 consensus positions) in special situations