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HMMER - Biological sequence analysis with profile hidden Markov models
Copyright (C) 2015 Howard Hughes Medical Institute.
------------------------------------------------------------------
Additional copyrights apply to the entirety of the package:
Copyright (C) 1992-2013 Sean R. Eddy
Copyright (C) 2000-2013 Howard Hughes Medical Institute
Copyright (C) 1992-2004 Washington University School of Medicine
Copyright (C) 1992-1994 MRC Laboratory of Molecular Biology
The code includes contributions and input from the members of the
HMMER development team and the Eddy/Rivas laboratories at HHMI Janelia
Farm, whose current members include:
Sean Eddy Janelia Farm
Sergi Castellano Janelia Farm
Goran Ceric Janelia Farm
Michael Farrar Janelia Farm
Rob Finn Janelia Farm
Bjarne Knudsen CLC bio
Diana Kolbe Washington University/Janelia Farm
Eric Nawrocki Janelia Farm
Elena Rivas Janelia Farm
Travis Wheeler Janelia Farm
HMMER also includes contributions from others, including copyrighted
and licensed code and technology. These are noted in the appropriate
places in source files. Contributors include:
Jeremy Buhler Washington University
Ian Holmes UC Berkeley
Erik Lindahl Stanford University
Graeme Mitchison Cambridge University
Lee Newberg Rensselaer Polytechnic Institute
Apple Computer Cupertino, CA
Free Software Foundation, Inc. Cambridge, MA
IBM TJ Watson Research Center Yorktown Heights, NY
X Consortium Cambridge, MA
HMMER uses the Easel software library, which has its own license and
copyright information. See easel/COPYRIGHT and easel/LICENSE.
HMMER includes patent-pending SIMD technology under nonexclusive
license from Michael Farrar. You are sublicensed to use this
technology specifically for the use, modification, and redistribution
of HMMER3, under the terms of the GPLv3 patent clause.
This source code is distributed under the terms of the GNU General
Public License. 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
your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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/>.
"HMMER" is a trademark of the Howard Hughes Medical Institute.
Although the code is freely available as open source, we intend that
only the version at http://hmmer.org/ is known as HMMER. You are free
to create a modified version and distribute it (subject to the terms
of the GPL), but we ask that you name it something that would not be
confused with HMMER itself.
------------------------------------------------------------------
The HMMER development team
HHMI Janelia Farm Research Campus
http://hmmer.org/
INSTALL
View file @ a0934cc0
Brief installation instructions
HMMER 3.1b2; February 2015
-------------------------------------------------------------
HMMER 3.2.1 (June 2018)
These are quick installation instructions. For complete documentation,
including customization and troubleshooting, please see the
Installation chapter in the HMMER User's Guide (Userguide.pdf).
Starting from a source distribution, hmmer-3.2.1.tar.gz:
uncompress hmmer-3.2.1.tar.gz
tar xf hmmer-3.2.1.tar
cd hmmer-3.2.1
./configure
make
make check # optional: automated tests
make install # optional: install HMMER programs and man pages
(cd easel; make install) # optional: install Easel tools too
-------------------------------------------------------------
For more details including customization, supported platforms, and
troubleshooting, see the Installation chapter in the HMMER User's
Guide (Userguide.pdf).
Starting from a distribution "with binaries", such as
hmmer-3.1b2-linux-intel-x86_64.tar.gz:
uncompress: uncompress hmmer-3.1b2-xyz.tar.gz
unpack: tar xf hmmer-3.1b2-xyz.tar
move into new directory: cd hmmer-3.1b2-xyz
The pre-compiled binaries are found in the directory ./binaries.
You may copy these into a directory of your choosing, or simply add
this directory to your $PATH variable.
-------------------------------------------------------------
Starting from a source distribution, hmmer-3.1b2.tar.gz:
uncompress: uncompress hmmer-3.1b2.tar.gz
unpack: tar xf hmmer-3.1b2.tar
move into new directory: cd hmmer-3.1b2
configure: ./configure
build: make
automated tests: make check
automated install: make install
-------------------------------------------------------------
HMMER is developed primarily on Linux and Mac OS/X systems. It is
tested on a variety of UNIX and UNIX-like operating systems. It is
written in ANSI C99 conforming to POSIX standards. It is meant to be
portable to any POSIX-compliant system with an ANSI C99 compiler,
including all UNIX and Macintosh systems. A binary version is also
available for Windows systems with Cygwin installed (Cygwin is
optional POSIX compatibility software).
-------------------------------------------------------------
Starting from a Subversion (SVN) working copy:
If you have checked HMMER 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
autoconf
(cd easel; autoconf)
-------------------------------------------------------------
The HMMER development team
HHMI Janelia Farm Research Campus
http://hmmer.org/
LICENSE
View file @ a0934cc0
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Makefile.in
View file @ a0934cc0
......@@ -6,11 +6,13 @@
# Optionally, you can run a test suite:
# % make check
#
# And optionally, you can install everything more permanently:
# Optionally, you can install programs and man pages more permanently:
# % make install
#
# For more information, see the Installation chapter of the HMMER
# User's Guide.
# Optionally, you can install some small tools ("miniapps") from our Easel library:
# % (cd easel; make install)
#
# For more information, see the Installation section in the User's Guide.
#
......@@ -52,9 +54,11 @@ man1ext = .1
# Compiler configuration
#
CC = @CC@
CFLAGS = @CFLAGS@ @PTHREAD_CFLAGS@ @PIC_FLAGS@
CFLAGS = @CFLAGS@
PTHREAD_CFLAGS = @PTHREAD_CFLAGS@
SSE_CFLAGS = @SSE_CFLAGS@
VMX_CFLAGS = @VMX_CFLAGS@
LDFLAGS = -static @LDFLAGS@
SIMDFLAGS = @SIMD_CFLAGS@
CPPFLAGS = @CPPFLAGS@
# Other tools
......@@ -68,33 +72,15 @@ INSTALL = @INSTALL@
QUIET_SUBDIR0 = +${MAKE} -C #space separator after -c
QUIET_SUBDIR1 =
ifndef V
QUIET = @
QUIET_CC = @echo ' ' CC $@;
QUIET_GEN = @echo ' ' GEN $@;
QUIET_AR = @echo ' ' AR $@;
QUIET_SUBDIR0 = +@subdir=
QUIET_SUBDIR1 = ; echo ' ' SUBDIR $$subdir; \
${MAKE} -C $$subdir
${MAKE} -s -C $$subdir
endif
# Programs installed by HMMER (stable, documented)
#
PROGS = alimask\
hmmalign\
hmmbuild\
hmmconvert\
hmmemit\
hmmfetch\
hmmpress\
hmmscan\
hmmsearch\
hmmsim\
hmmstat\
jackhmmer\
phmmer\
nhmmer\
nhmmscan\
hmmpgmd
.PHONY: all dev check pdf install uninstall clean distclean TAGS
# all: Compile all documented executables.
......@@ -134,25 +120,25 @@ check:
pdf:
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} pdf
# install: installs the binaries in ${bindir}/
# When man pages are done, will install man pages in MANDIR/man1/ (e.g. if MANSUFFIX is 1)
# install: binaries in ${bindir}/, man pages in ${man1dir}/
# Creates these directories if they don't exist.
# Prefix those paths with ${DESTDIR} (rarely used, usually null;
# may be set on a make command line when building contrib RPMs).
#
# Prefix paths with optional ${DESTDIR}, which
# downstream packagers may set on make command line when
# building packages.
#
# Does not use quiet beautification magic; always verbose.
install:
${INSTALL} -d ${DESTDIR}${bindir}
${INSTALL} -d ${DESTDIR}${libdir}
${INSTALL} -d ${DESTDIR}${includedir}
${INSTALL} -d ${DESTDIR}${man1dir}
${INSTALL} -d ${DESTDIR}${pdfdir}
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} install
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} install
${MAKE} -C src install
${MAKE} -C documentation install
# uninstall: Reverses the steps of "make install".
# uninstall: reverses the steps of "make install".
#
uninstall:
${QUIET_SUBDIR0}src ${QUIET_SUBDIR1} uninstall
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} uninstall
${MAKE} -C src uninstall
${MAKE} -C documentation uninstall
# "make clean" removes almost everything except configuration files.
#
......@@ -163,7 +149,10 @@ clean:
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} clean
${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} clean
-rm -f *.o *~ Makefile.bak core TAGS gmon.out
${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
ifndef V
@echo ' ' CLEAN hmmer
endif
# "make distclean" leaves a pristine source distribution.
#
......@@ -174,82 +163,18 @@ distclean:
${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
${QUIET_SUBDIR0}${ESLDIR} ${QUIET_SUBDIR1} distclean
${QUIET_SUBDIR0}${SADIR} ${QUIET_SUBDIR1} distclean
-rm config.log config.status
-rm -rf autom4te.cache
-rm -f *.o *~ Makefile.bak core TAGS gmon.out
-rm -f cscope.po.out cscope.out cscope.in.out cscope.files
-rm -f src/impl
-rm Makefile
#Use 'ifneq' instead of 'test -e' because the '+@' in QUIET_SUBDIR0 can't
#be passed to the shell. Note that ifneq breaks if indented.
ifneq (,$(wildcard ./release-notes/LICENSE.sh))
-rm -f release-notes/LICENSE.sh
${QUIET}-rm config.log config.status
${QUIET}-rm -rf autom4te.cache
${QUIET}-rm -f *.o *~ Makefile.bak core TAGS gmon.out
${QUIET}-rm -f cscope.po.out cscope.out cscope.in.out cscope.files
${QUIET}-rm -f src/impl
${QUIET}-rm Makefile
ifndef V
@echo ' ' CLEAN hmmer
endif
TAGS:
-rm -f ${top_srcdir}/TAGS
make tags-append
tags-append:
etags -o ${top_srcdir}/TAGS -a ${srcdir}/Makefile.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/COPYRIGHT
etags -o ${top_srcdir}/TAGS -a ${srcdir}/INSTALL
etags -o ${top_srcdir}/TAGS -a ${srcdir}/LICENSE
etags -o ${top_srcdir}/TAGS -a ${srcdir}/README
etags -o ${top_srcdir}/TAGS -a ${srcdir}/configure.ac
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.h
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/*.pl
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_sse/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_sse/*.h
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_sse/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_dummy/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_dummy/*.h
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_dummy/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_vmx/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_vmx/*.h
etags -o ${top_srcdir}/TAGS -a ${srcdir}/src/impl_vmx/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/man/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/man/*.man
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/man/boilerplate-tail
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/userguide/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/documentation/userguide/*.tex
etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/README
etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/libdivsufsort/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/00README
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/*.c
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/x-*
etags -o ${top_srcdir}/TAGS -a ${srcdir}/profmark/pmark-*
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.in
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.pl
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.sh
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.pm
etags -o ${top_srcdir}/TAGS -a ${srcdir}/testsuite/*.sqc
${QUIET_SUBDIR0}easel ${QUIET_SUBDIR1} tags-append
################################################################
# HMMER - Biological sequence analysis with profile HMMs
# Version 3.1b2; February 2015
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Other copyrights also apply. See the COPYRIGHT file for a full list.
#
# HMMER is distributed under the terms of the GNU General Public License
# (GPLv3). See the LICENSE file for details.
#
# SVN $URL: https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/3.1/Makefile.in $
# SVN $Id: Makefile.in 4489 2013-06-19 02:46:43Z wheelert $
################################################################
./makeTAGS.sh
README deleted 100644 → 0
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HMMER - profile hidden Markov models for biological sequence analysis
http://hmmer.org/
Version 3.1b2; February 2015
Copyright (C) 2015 Howard Hughes Medical Institute.
------------------------------------------------------------------
HMMER searches biological sequence databases for homologous sequences,
using either single sequences or multiple sequence alignments as
queries. HMMER implements a technology called "profile hidden Markov
models" (profile HMMs). HMMER is the software engine underlying many
protein family domain databases and large-scale annotation pipelines,
including the Pfam and SMART databases.
Other files to read in the top-level source directory:
INSTALL Brief installation instructions.
Userguide.pdf The HMMER 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
HMMER User's Guide (Userguide.pdf).
-------------------------------------------------------------------
The HMMER development team
HHMI Janelia Farm Research Campus
http://hmmer.org/
README.md 0 → 100644
View file @ a0934cc0
## HMMER - biological sequence analysis using profile HMMs
[HMMER](http://hmmer.org) searches biological sequence databases for
homologous sequences, using either single sequences or multiple
sequence alignments as queries. HMMER implements a technology called
"profile hidden Markov models" (profile HMMs). HMMER is used by many
protein family domain databases and large-scale annotation pipelines,
including [Pfam](http://pfam.xfam.org) and other members of the
[InterPro Consortium](http://www.ebi.ac.uk/interpro/).
To obtain HMMER releases, please visit [hmmer.org](http://hmmer.org).
To participate in HMMER development, visit us at
[github](https://github.com/EddyRivasLab/hmmer). HMMER development
depends on the Easel library, also at
[github](https://github.com/EddyRivasLab/easel).
### to download and build the current source code release:
```
% wget http://eddylab.org/software/hmmer/hmmer.tar.gz
% tar zxf hmmer.tar.gz
% cd hmmer-3.2.1
% ./configure --prefix /your/install/path
% make
% make check # optional: run automated tests
% make install # optional: install HMMER programs, man pages
% (cd easel; make install) # optional: install Easel tools
```
Executable programs will be installed in `/your/install/path/bin`. If
you leave this optional `./configure` argument off, the default prefix
is `/usr/local`.
Files to read in the source directory:
* INSTALL - brief installation instructions.
* Userguide.pdf - the HMMER User's Guide.
To get started after installation, see the Tutorial section in the
HMMER User's Guide (Userguide.pdf).
### to clone a copy of HMMER3 source from github:
The tarball way, above, is a better way to install HMMER (it includes
a precompiled Userguide.pdf, for example), but you can also clone our
github repo. You need to clone both the HMMER and Easel repositories,
as follows:
```
% git clone https://github.com/EddyRivasLab/hmmer
% cd hmmer
% git clone https://github.com/EddyRivasLab/easel
% autoconf
```
and to build:
```bash
% ./configure
% make
```
Our [git workflow](https://github.com/EddyRivasLab/hmmer/wiki/Git-workflow)
includes three main branches:
* **master** is the stable branch for HMMER3 releases (including when
H3 is released as a library inside Infernal)
* **develop** is the HMMER3 development branch
* **h4-develop** is the HMMER4 development branch.
To build the most recent official release, leave both HMMER and Easel
on their default **master** branch. To contribute to HMMER3
development, you want to be on the **develop** branches.
### to report a problem:
Visit our
[issues tracking page at github](https://github.com/EddyRivasLab/hmmer/issues).
RELEASE-3.2.1 0 → 100644
View file @ a0934cc0
HMMER 3.2.1 release notes (Jun 2018)
http://hmmer.org
Release 3.2.1 fixes:
----------------------
* iss #142: compilation fails ungracefully on unsupported ppc64le
* iss #140: jackhmmer --fast segfault. Removes --fast
and --symfrac options from jackhmmer and its documentation.
* iss #141, #120: compilation failures on i586, ppc64be.
* iss #132: hmmbuild miscounts transitions in final node.
Release notes for 3.2:
-----------------------
Larger changes:
* HMMER is now distributed under the BSD license, instead of the GPL.
* The 'make install' has been streamlined. Now we install only
programs and man pages, for 18 HMMER programs and 22 Easel miniapps.
We don't install development .h headers or .a libraries.
* We changed our default policy on the number of threads/cores that
the search programs use. Previously multithreaded programs would use
all available cores by default; now we use two worker threads by
default (~2 cores), if multiple cores are available. HMMER3 search
programs do not scale much beyond 2 cores anyway, due to input
saturation and memory use.
* H3 now strictly requires either SSE2 or Altivec/VMX vector
support. The portable 'dummy' implementation has been removed. This
was an non-vectorized portable pure C implementation, much slower
than HMMER3 on x86 and PowerPC platforms with SSE2 or Altivec/VMX
vector instructions. We had included it because we could -- HMMER3
implements "generic" non-vectorized versions of its core algorithms
for unit testing purposes anyway. We thought maybe it'd be useful.
As far as I can tell, it was never useful, but several packagers on
non-x86, non-PowerPC platforms packaged and distributed it, ignoring
the prominent health warnings we put on it.
Smaller new features include:
* improved documentation of --mxfile and score matrix file format
* adds support for EBI's "uncheck all hits" on jackhmmer web site
* removed experimental hmmbuild --seq_weights_r and --seq_weights_e options
* appeased new gcc6 --Wmisleading-indentation warning
* SSI indexing is now robust against duplicate keys
* autoconf now robust against someone running gnu `autoheader`
* improved autoconf of SIMD vector support
* improved autoconf of DAZ,FTZ support on x86 processors
* improved autodetection of phylip interleaved vs sequential format
* improved autodetection of A2M vs. aligned FASTA format
* clarified A2M format parse error when file contains 'O' residue
* improved portability to Intel/Solaris
* FASTA parser now ignores description line after a ctrl-A
* MSAs output with -A option now include name, acc, desc, author markup.
* In Easel miniapps, esl-translate replaces previous (buggy) esl-stranslate.
* Easel miniapps include esl-alirev, reverse complementing RNA/DNA alignment
* nhmmer/nhmmscan now allow alignments as target dbs
* target relentropy for DNA models changed from 0.45 to 0.62
* updated the User Guide
Fixed bugs include:
* nhmmscan faulted on old model files because it expected MAXL field
* --cut-ga wasn't checking that GA line was actually present in model
* GA thresholds weren't being captured from DNA/RNA Stockholm alignments
* A2M alignment parsing was corrupted on lines ending in insertions
* alphabet-guessing failed for FASTA seq >4096 bytes and <4000 residues
* genbank to fasta format conversion was leaving extra \n in accession
* NCBI db format: multithreaded nhmmer was failing to read
* NCBI db format: 1st database sequence was skipped for second query (#e6)
* unit test failures in esl_normal, esl_random due to floating point math
* nhmmer was corrupted by * symbols in input sequence (iss#118)
* hmmsearch -A crashed if top-ranked hit has no domains (iss#131)
* new variety of "backconverted subseq" hmmsearch crash on *'s (iss#135)
* qsort() callbacks now return -1/0/1 as they should. (Infernal iss#11)
* esl_buffer hangs when input ends with \r (Easel iss#23)
For details, you can view and search our issue tracking logs at github:
https://github.com/EddyRivasLab/hmmer/issues/ for HMMER itself
https://github.com/EddyRivasLab/easel/issues/ for the underlying Easel library
Userguide.pdf
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{}
\ No newline at end of file
documentation/Makefile.in
View file @ a0934cc0
......@@ -7,7 +7,7 @@ QUIET_SUBDIR1 =
ifndef V
QUIET_SUBDIR0 = +@subdir=
QUIET_SUBDIR1 = ; echo ' ' SUBDIR $$subdir; \
${MAKE} -C $$subdir
${MAKE} -s -C $$subdir
endif
......@@ -16,38 +16,27 @@ endif
pdf:
${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} pdf
# install, uninstall are always verbose; do not use quiet beautification
install:
${QUIET_SUBDIR0}man ${QUIET_SUBDIR1} install
${MAKE} -C man install
uninstall:
${QUIET_SUBDIR0}man ${QUIET_SUBDIR1} uninstall
${MAKE} -C man uninstall
clean:
#Use 'ifneq' instead of 'test -e' because the '+@' in QUIET_SUBDIR0 can't
#be passed to the shell. Note that ifneq breaks if indented.
ifneq (,$(wildcard userguide/.))
${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} clean
endif
${QUIET_SUBDIR0}man ${QUIET_SUBDIR1} clean;
${QUIET_SUBDIR0}man ${QUIET_SUBDIR1} clean
-rm -f *~
ifndef V
@echo ' ' CLEAN documentation
endif
distclean:
#See above for explanation of 'ifneq' usage
ifneq (,$(wildcard userguide/.))
${QUIET_SUBDIR0}userguide ${QUIET_SUBDIR1} distclean
endif
${QUIET_SUBDIR0}man ${QUIET_SUBDIR1} distclean
-rm -f *~
-rm -f Makefile
################################################################
# HMMER - Biological sequence analysis with profile HMMs
# Version 3.1b2; February 2015
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Other copyrights also apply. See the COPYRIGHT file for a full list.
#
# HMMER is distributed under the terms of the GNU General Public License
# (GPLv3). See the LICENSE file for details.
#
# SVN $URL: https://svn.janelia.org/eddylab/eddys/src/hmmer/branches/3.1/documentation/Makefile.in $
# SVN $Id: Makefile.in 4489 2013-06-19 02:46:43Z wheelert $
################################################################
ifndef V
@echo ' ' CLEAN documentation
endif
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{}
\ No newline at end of file
documentation/man/Makefile.in
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......@@ -44,7 +44,7 @@ MANS = hmmer\
install:
for file in ${MANS}; do \
${INSTALL} -m 0755 ${srcdir}/$$file.man ${DESTDIR}${man1dir}/$${file}${man1ext} ;\
${INSTALL} -m 0664 $$file.man ${DESTDIR}${man1dir}/$${file}${man1ext} ;\
done
uninstall:
......@@ -54,20 +54,12 @@ uninstall:
clean:
-rm -f *~
ifndef V
@echo ' ' CLEAN man
endif
distclean:
-rm -f *~
-rm -f *.man
-rm -f Makefile
################################################################
# HMMER - Biological sequence analysis with profile HMMs
# Version 3.1b2; February 2015
# Copyright (C) 2015 Howard Hughes Medical Institute.
# Other copyrights also apply. See the COPYRIGHT file for a full list.
#
# HMMER is distributed under the terms of the GNU General Public License
# (GPLv3). See the LICENSE file for details.
#
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documentation/man/alimask.man → documentation/man/alimask.man.in
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.TH "alimask" 1 "February 2015" "HMMER 3.1b2" "HMMER Manual"
.TH "alimask" 1 "@HMMER_DATE@" "HMMER @HMMER_VERSION@" "HMMER Manual"
.SH NAME
alimask - Add mask line to a multiple sequence alignment
alimask \- calculate and add column mask to a multiple sequence alignment
.SH SYNOPSIS
.B alimask
.I [options]
.I <msafile>
.I <postmsafile>
[\fIoptions\fR]
.I msafile
.I postmsafile
.SH DESCRIPTION
......@@ -27,7 +27,7 @@ altered, even in masked regions.
.B alimask
autodetects input format, and produces masked alignments
in Stockholm format.
.I <msafile>
.I msafile
may contain only one sequence alignment.
.PP
......@@ -39,14 +39,14 @@ hits.
.PP
In the simplest case, a mask range is given in coordinates
relative to the input alignment, using
.BI --alirange " <s>".
.BI \-\-alirange " <s>".
However it is more often the case that the region to be
masked has been identified in coordinates relative to
the profile model (e.g. based on recognizing a simple
repeat pattern in false hit alignments or in the HMM logo).
Not all alignment columns are converted to match state
positions in the profile (see the
.I --symfrac
.B \-\-symfrac
flag for
.B hmmbuild
for discussion), so model positions do not necessarily match
......@@ -56,7 +56,7 @@ alignment positions,
.B alimask
accepts the mask range input in model coordinates as well,
using
.BI --modelrange " <s>".
.BI \-\-modelrange " <s>".
When using this flag,
.I alimask
determines which alignment positions would be identified by
......@@ -75,47 +75,46 @@ flags are also used by
.SH OPTIONS
.TP
.B -h
.B \-h
Help; print a brief reminder of command line usage and all available
options.
.TP
.BI -o " <f>"
.BI \-o " <f>"
Direct the summary output to file
.IR <f> ,
rather than to
.IR stdout .
rather than to stdout.
.SH OPTIONS FOR SPECIFYING MASK RANGE
A single mask range is given as a dash-separated pair, like
.I "--modelrange 10-20"
.B "\-\-modelrange 10\-20"
and multiple ranges may be submitted as a comma-separated list,
.IR "--modelrange 10-20,30-42" .
.BR "\-\-modelrange 10\-20,30\-42" .
.TP
.BI --modelrange " <s>"
.BI \-\-modelrange " <s>"
Supply the given range(s) in model coordinates.
.TP
.BI --alirange " <s>"
.BI \-\-alirange " <s>"
Supply the given range(s) in alignment coordinates.
.TP
.B --apendmask
.B \-\-apendmask
Add to the existing mask found with the alignment.
The default is to overwrite any existing mask.
.TP
.BI --model2ali " <s>"
.BI \-\-model2ali " <s>"
Rather than actually produce the masked alignment, simply
print model range(s) corresponding to input alignment
range(s).
.TP
.BI --ali2model " <s>"
.BI \-\-ali2model " <s>"
Rather than actually produce the masked alignment, simply
print alignment range(s) corresponding to input model
range(s).
......@@ -123,34 +122,23 @@ range(s).
.SH OPTIONS FOR SPECIFYING THE ALPHABET
The alphabet type (amino, DNA, or RNA) is autodetected by default, by
looking at the composition of the
.IR msafile .
Autodetection is normally quite reliable, but occasionally alphabet
type may be ambiguous and autodetection can fail (for instance, on
tiny toy alignments of just a few residues). To avoid this, or to
increase robustness in automated analysis pipelines, you may specify
the alphabet type of
.I msafile
with these options.
.TP
.B --amino
Specify that all sequences in
.B \-\-amino
Assert that sequences in
.I msafile
are proteins.
are protein, bypassing alphabet autodetection.
.TP
.B --dna
Specify that all sequences in
.B \-\-dna
Assert that sequences in
.I msafile
are DNAs.
are DNA, bypassing alphabet autodetection.
.TP
.B --rna
Specify that all sequences in
.B \-\-rna
Assert that sequences in
.I msafile
are RNAs.
are RNA, bypassing alphabet autodetection.
......@@ -159,24 +147,24 @@ are RNAs.
These options control how consensus columns are defined in an alignment.
.TP
.B --fast
.B \-\-fast
Define consensus columns as those that have a fraction >=
.B symfrac
of residues as opposed to gaps. (See below for the
.B --symfrac
.B \-\-symfrac
option.) This is the default.
.TP
.B --hand
.B \-\-hand
Define consensus columns in next profile using reference annotation to
the multiple alignment.
This allows you to define any consensus columns you like.
.TP
.BI --symfrac " <x>"
.BI \-\-symfrac " <x>"
Define the residue fraction threshold necessary to define a
consensus column when using the
.B --fast
.B \-\-fast
option. The default is 0.5. The symbol fraction in each column
is calculated after taking relative sequence weighting into account,
and ignoring gap characters corresponding to ends of sequence
......@@ -188,7 +176,7 @@ means that only columns that include 0 gaps (internal
insertions/deletions) will be assigned as consensus.
.TP
.BI --fragthresh " <x>"
.BI \-\-fragthresh " <x>"
We only want to count terminal gaps as deletions if the aligned
sequence is known to be full-length, not if it is a fragment (for
instance, because only part of it was sequenced). HMMER uses a simple
......@@ -198,12 +186,12 @@ or equal to a fraction
times the alignment length in columns,
then the sequence is handled as a fragment. The default is 0.5.
Setting
.BI --fragthresh 0
.B \-\-fragthresh 0
will define no (nonempty) sequence as a fragment; you might want to do
this if you know you've got a carefully curated alignment of full-length
sequences.
Setting
.BI --fragthresh 1
.B \-\-fragthresh 1
will define all sequences as fragments; you might want to do this if
you know your alignment is entirely composed of fragments, such as
translated short reads in metagenomic shotgun data.
......@@ -219,34 +207,34 @@ each receive half the weight that one sequence would. These options
control which algorithm gets used.
.TP
.B --wpb
.B \-\-wpb
Use the Henikoff position-based sequence weighting scheme [Henikoff
and Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default.
.TP
.B --wgsc
.B \-\-wgsc
Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et
al, J. Mol. Biol. 235:1067, 1994].
.TP
.B --wblosum
.B \-\-wblosum
Use the same clustering scheme that was used to weight data in
calculating BLOSUM subsitution matrices [Henikoff and Henikoff,
Proc. Natl. Acad. Sci 89:10915, 1992]. Sequences are single-linkage
clustered at an identity threshold (default 0.62; see
.IR --wid )
.BR \-\-wid )
and within each cluster of c sequences, each sequence gets relative
weight 1/c.
.TP
.B --wnone
.B \-\-wnone
No relative weights. All sequences are assigned uniform weight.
.TP
.BI --wid " <x>"
.BI \-\-wid " <x>"
Sets the identity threshold used by single-linkage clustering when
using
.IR --wblosum .
.BR \-\-wblosum .
Invalid with any other weighting scheme. Default is 0.62.
......@@ -256,19 +244,52 @@ Invalid with any other weighting scheme. Default is 0.62.
.SH OTHER OPTIONS
.TP
.BI --informat " <s>"
Declare that the input
.BI \-\-informat " <s>"
Assert that input
.I msafile
is in format
is in alignment format
.IR <s> ,
bypassing format autodetection.
Common choices for
.I <s>
include:
.BR stockholm ,
.BR a2m ,
.BR afa ,
.BR psiblast ,
.BR clustal ,
.BR phylip .
For more information, and for codes for some less common formats,
see main documentation.
The string
.I <s>
is case-insensitive (\fBa2m\fR or \fBA2M\fR both work).
.TP
.BI \-\-outformat " <s>"
Write the output
.I postmsafile
in alignment format
.IR <s> .
Currently the accepted multiple alignment sequence file formats
include Stockholm, Aligned FASTA, Clustal, NCBI PSI-BLAST, PHYLIP,
Selex, and UCSC SAM A2M. Default is to autodetect the format of
the file.
Common choices for
.I <s>
include:
.BR stockholm ,
.BR a2m ,
.BR afa ,
.BR psiblast ,
.BR clustal ,
.BR phylip .
The string
.I <s>
is case-insensitive (\fBa2m\fR or \fBA2M\fR both work).
Default is
.BR stockholm .
.TP
.BI --seed " <n>"
.BI \-\-seed " <n>"
Seed the random number generator with
.IR <n> ,
an integer >= 0.
......@@ -287,37 +308,33 @@ The default seed is 42.
.SH SEE ALSO
See
.B hmmer(1)
.BR hmmer (1)
for a master man page with a list of all the individual man pages
for programs in the HMMER package.
.PP
For complete documentation, see the user guide that came with your
HMMER distribution (Userguide.pdf); or see the HMMER web page
().
(@HMMER_URL@).
.SH COPYRIGHT
.nf
Copyright (C) 2015 Howard Hughes Medical Institute.
Freely distributed under the GNU General Public License (GPLv3).
@HMMER_COPYRIGHT@
@HMMER_LICENSE@
.fi
For additional information on copyright and licensing, see the file
called COPYRIGHT in your HMMER source distribution, or see the HMMER
web page
().
(@HMMER_URL@).
.SH AUTHOR
.nf
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org
.fi
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.SH SEE ALSO
See
.B hmmer(1)
for a master man page, with full list of the individual man pages
for all programs in the HMMER package.
.PP
For complete documentation, see the user guide that came with your
HMMER distribution (Userguide.pdf); or see the HMMER web page
(@HMMER_URL@).
.SH COPYRIGHT
.nf
@HMMER_COPYRIGHT@
@HMMER_LICENSE@
.fi
For additional information on copyright and licensing, see the file
called COPYRIGHT in your HMMER source distribution, or see the HMMER
web page
(@HMMER_URL@).
.SH AUTHOR
.nf
Sean Eddy
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org
.fi