MutationsHunter

MutationsHunter is a Python wrapper for three different softwares: InParanoid, FASTA and PAML. It allows the calculation of the dN/dS ratio (ratio between non-synonymous and synonymous substitutions rates) between diverging coding sequences (i.e., orthologs or paralogs genes). This is a base information for comparative genomics; the hypothesis is that a low ratio (< 1) is associated to negatively selected genes (ie. genes where the sequence is conserved), while a high one is associated to positively selected ones (ie. genes without strong conservation).

References:

Remm M, Storm CEV and Sonnhammer ELL (2001). Automatic Clustering of Orthologs and In-paralogs from Pairwise Species Comparisons. JMB, 314:1041-1052. http://inparanoid.cgb.ki.se/
W. R. Pearson and D. J. Lipman (1988). Improved Tools for Biological Sequence Analysis. PNAS 85:2444-2448 http://www.people.virginia.edu/~wrp/pearson.html
Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood Computer Applications in BioSciences 13:555-556 http://abacus.gene.ucl.ac.uk/software/paml.html

Version

0.1 (Oct 22, 2005)

Documentation

The documentation is included in the package below, in format.

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MutationsHunter 0.1 — October 22, 2005 Download (13.3 KB)