Difference between revisions of "CoMap"

Latest revision as of 18:39, 12 August 2022

Description

comap website

CoMap implements evolution-based detection of co-evolving positions in a molecule.

CoMap performs the following tasks:

Compute probabilistic substitution maps
Test for pairs/groups of sites that do not evolve independently

Environment Modules

Run module spider comap to find out what environment modules are available for this application.

System Variables

HPC_COMAP_DIR - installation directory

Citation

If you publish research that uses comap you have to cite it as follows:

Cite the following article if you use the pairwise method

Dutheil J, Pupko T, Jean-Marie A, Galtier N.

A model-based approach for detecting coevolving positions in a molecule.

Mol Biol Evol. 2005 Sep;22(9):1919-28.

Cite the following article if you use the clustering method

Dutheil J, Galtier N.

Detecting groups of co-evolving positions in a molecule: a clustering approach.

BMC Evol Biol. 2007 Nov 30;7(1):242

Cite the following article if you use the candidate approach method

Dutheil JY, Jossinet F, Westhof E.

Base pairing constraints drive structural epistasis in ribosomal RNA sequences.

Mol Biol Evol. 2010 Aug;27(8):1868-76

MICA and the new p-value computation algorithm are described in:

Dutheil JY. Detecting coevolving positions in a molecule: why and how to account for phylogeny. Brief Bioinform. 2011 Sep 24.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]]
+[[Category:Software]][[Category:Biology]][[Category:Genomics]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|comap}}
@@ Line 10: / Line 10: @@
 |{{#vardefine:testing|}}       <!--PROFILING-->
 |{{#vardefine:faq|}}             <!--FAQ-->
-|{{#vardefine:citation|}}       <!--CITATION-->
+|{{#vardefine:citation|1}}       <!--CITATION-->
 |{{#vardefine:installation|}} <!--INSTALLATION-->
 |}
@@ Line 25: / Line 25: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-===Serial===
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 65: / Line 55: @@
 {{#if: {{#var: citation}}|==Citation==
 If you publish research that uses {{#var:app}} you have to cite it as follows:
-WRITE_CITATION_HERE
+;Cite the following article if you use the pairwise method:
+Dutheil J, Pupko T, Jean-Marie A, Galtier N.
+A model-based approach for detecting coevolving positions in a molecule.
+Mol Biol Evol. 2005 Sep;22(9):1919-28.
+;Cite the following article if you use the clustering method:
+Dutheil J, Galtier N.
+Detecting groups of co-evolving positions in a molecule: a clustering approach.
+BMC Evol Biol. 2007 Nov 30;7(1):242
+;Cite the following article if you use the candidate approach method:
+Dutheil JY, Jossinet F, Westhof E.
+Base pairing constraints drive structural epistasis in ribosomal RNA sequences.
+Mol Biol Evol. 2010 Aug;27(8):1868-76
+MICA and the new p-value computation algorithm are described in:
+Dutheil JY.
+Detecting coevolving positions in a molecule: why and how to account for phylogeny.
+Brief Bioinform. 2011 Sep 24.
 |}}
 <!--Installation-->