HMMER - Revision history

Joel Hedlund (NSC): /* Compilation */

2013-04-23T08:27:45Z

‎Compilation

Joel Hedlund (NSC) at 16:42, 21 September 2011

2011-09-21T16:42:10Z

Joel Hedlund (NSC) at 18:12, 9 September 2011

2011-09-09T18:12:54Z

Joel Hedlund (NSC) at 17:52, 9 September 2011

2011-09-09T17:52:53Z

Joel Hedlund (NSC): /* Versions */

2011-09-09T17:52:33Z

‎Versions

Joel Hedlund (NSC) at 13:37, 9 September 2011

2011-09-09T13:37:53Z

Joel Hedlund (NSC) at 13:36, 9 September 2011

2011-09-09T13:36:07Z

Joel Hedlund (NSC) at 13:35, 9 September 2011

2011-09-09T13:35:27Z

Joel Hedlund (NSC): /* Availability */

2011-09-09T13:24:56Z

‎Availability

Joel Hedlund (NSC) at 13:17, 9 September 2011

2011-09-09T13:17:26Z

@@ Line 55: / Line 55: @@
 HMMER-2 is also extremely sensitive to hardware vectorisation optimisations, even to the extent that -xSSE4.2 produces significantly faster binaries than does -xSSE4.1, so it makes sense to set this as aggressively as possible. NSC uses icc 11.1.069 and <code>CFLAGS="-O3 -ip -xSSE4.2"</code> for the SNIC systems [http://www.nsc.liu.se/systems/snic/ Kappa] and [http://www.nsc.liu.se/systems/snic/ Matter], and <code>CFLAGS="-O3 -ip -xSSSE3"</code> for [http://www.nsc.liu.se/systems/snic/ Neolith].
-The official binary distribution of HMMER-3.0 is compiled with icc, and is fully adequate for threaded operation. However, some of the HMMER-3 binaries (e.g. hmmscan) have been shown to perform upward of 50% better with MPI parallelisation, so this may constitute reason to recompile locally. It may also be profitable to carefully select MPI library, as intelmpi in standard configuration can give fluctuations in runtime upwards of +~100% with hmmsearch, while openmpi seemingly performs optimally and consistently. For HMMER-3, [http://www.nsc.liu.se NSC] uses icc 11.1.069 and openmpi 1.4.1, and uses the compilator flags automatically detected by the configure script.
+The official binary distribution of HMMER-3.0 is compiled with icc, and is fully adequate for threaded operation. However, some of the HMMER-3 binaries (e.g. hmmscan) have been shown to perform upward of 50% better with MPI parallelisation, so this may constitute reason to recompile locally. It may also be profitable to carefully select MPI library, as intelmpi in standard configuration can give fluctuations in runtime upwards of +~100% with hmmsearch, while openmpi seemingly performs optimally and consistently. For HMMER-3, [http://www.nsc.liu.se NSC] uses icc 11.1.069 and openmpi 1.4.1, and uses the compiler flags automatically detected by the configure script.
 == License ==

@@ Line 5: / Line 5: @@
 }}
 [http://hmmer.janelia.org {{PAGENAME}}] is a software {{#show: {{PAGENAME}} |?description}} of known regions in proteins.
 == General info ==
@@ Line 53: / Line 56: @@
 The official binary distribution of HMMER-3.0 is compiled with icc, and is fully adequate for threaded operation. However, some of the HMMER-3 binaries (e.g. hmmscan) have been shown to perform upward of 50% better with MPI parallelisation, so this may constitute reason to recompile locally. It may also be profitable to carefully select MPI library, as intelmpi in standard configuration can give fluctuations in runtime upwards of +~100% with hmmsearch, while openmpi seemingly performs optimally and consistently. For HMMER-3, [http://www.nsc.liu.se NSC] uses icc 11.1.069 and openmpi 1.4.1, and uses the compilator flags automatically detected by the configure script.
 == License ==

@@ Line 3: / Line 3: @@
 |license=free
 |fields=bioinformatics
 }}
 [http://hmmer.janelia.org {{PAGENAME}}] is a software {{#show: {{PAGENAME}} |?description}} of known regions in proteins.

@@ Line 6: / Line 6: @@
 }}
 [http://hmmer.janelia.org {{PAGENAME}}] is a software {{#show: {{PAGENAME}} |?description}} of known regions in proteins.
 == General info ==
@@ Line 63: / Line 60: @@
 == License ==
 {{show license}}
 == Links ==

@@ Line 28: / Line 28: @@
 * HMMER-3.0: Fast, but backwards incompatible and non-feature-complete.
-Their implementations and output (and potentially also the actual results) are vastly different, so ongoing projects are not recommended to switch between them. For new project, it is highly recommended to spend some time to deduce which version is the most suitable.
+Their implementations and output (and potentially also the actual results) are vastly different, so ongoing projects are not recommended to switch between them. For new projects, it is highly recommended to spend some time to deduce which version is the most suitable.
 HMMER-3 may seem like an obvious choice; it is much faster than its predecessor and it is currently used in large scale production (e.g. by [http://pfam.sanger.ac.uk/ Pfam]), and it is also promoted as the official main HMMER version. However, HMMER-3.0 is not feature complete. Especially, the old default alignment behavior (glocal, hmm_ls) is missing, so if this feature is necessary: choose HMMER-2.3.2.
 == Computational considerations ==

@@ Line 60: / Line 60: @@
 == Availability ==
-{{list resources for software}}
+{{list resources for software devel}}
 == License ==

@@ Line 1: / Line 1: @@
-{{software info
+{{software info devel
 |description=package for working with profile hidden Markov models (HMM)
 |license=free
 |fields=bioinformatics
-|resources=kappa;matter;neolith;akka;kalkyl
+|resources=kappa;<math>Insert formula here</math>matter;neolith;akka;kalkyl
 }}
 [http://hmmer.janelia.org {{PAGENAME}}] is a software {{#show: {{PAGENAME}} |?description}} of known regions in proteins.