Recombination detection from command line?

Question

[Adrian Pelin]

Hello,

I have many fasta alignments between a few sequences, and I want to test them for presence of recombination. RDP seems really glitched and trying 8 different version they all seem to crash. Is there anything that can do a similar job on a Linux command line system?

Answer 1

[Giovanni M Dall'Olio]

You may try with LDhat. I am not sure if there are newer software to estimate recombination, but LDhat should be fine if you only need an estimation.

For more information on how to run LDhat, check the manual on its webpage. In short, you need to run first the convert executable to generate a .locus and a .sites files. Then, use pairwise or one of the other models (see the manual) to estimate the recombination rates.