## Do I need omegaMap?

Recombination in your sample of genes causes the evolutionary tree to change along the sequence. That violates the assumption of phylogenetic methods that there is a single tree for the sequence. Simulation studies [1, 2, 3] have shown that can have unexpected effects on inference, and in the case of detecting positive selection, can cause false positive rates up to 90%. omegaMap is a method for estimating variation in selection pressure along a sequence in the presence of recombination [4].

### Has there been recombination in my sequences?

A simple permutation test can rapidly detect recombination in a set of DNA or RNA
sequences. The program `permute` gives a p value for the null hypothesis of
no recombination in your data. If the p value is significant (*p* < 0.05) then
recombination is detectable in your sequences and you should not apply phylogenetic-based
methods to the data. More on how `permute` works.

`permute file.txt`

or

`permute file.txt 999`

where `file.txt` is the name of your FASTA format sequence file, and `999`
is the number of permutations. If omitted, the default is 999 permutations. The output
will look something like this:

### Download permute

`permute` can be downloaded as a ready-to-use executable or as source code using
the links below.

- Download ready-to-use executables
- Download source code
- Bugs and version information
- Back to software

### References

- Schierup, M. H., and J. Hein (2000)

**Consequences of recombination on traditional phylogenetic analysis.**

*Genetics*156: 879-891. - Anisimova, M., R. Nielsen and Z. Yang (2003)

**Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.**

*Genetics*164: 1229-1236. - Shriner, D., D. C. Nickle, M. A. Jensen and J. I. Mullins (2003)

**Potential impact of recombination on sitewise approaches for detecting positive natural selection.**

*Genetical Research*81: 115-121. - Wilson, D. J. and G. McVean (2006)

**Estimating diversifying selection and functional constraint in the presence of recombination.**

*Genetics*172: 1411-1425.