Difference between revisions of "CoMap"
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==System Variables== | ==System Variables== | ||
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If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} 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. | ||
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| + | =Validation= | ||
| + | * Validated 4/5/2018 | ||
Revision as of 21:07, 6 December 2019
Description
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
Required Modules
Serial
- comap
System Variables
- HPC_COMAP_DIR
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.
Validation
- Validated 4/5/2018