LDHAT pairwise analysis to test for recombination

Question

[ch_at]

Hi,

I am using the program LDHATv2.2a for testing for recombination.

I have used an alignment in FASTA format(myseqs.fasta) and used the command

./convert -seq myseqs.fasta

to obtain the sites.txt and locs.txt file.

After this I did

./pairwise -seq myseqs.fasta -loc locs.txt

using the locs.txt file that was created using the convert command and my original FASTA file myseqs.fasta.

However this didn't work and I got the following error:

...
Sequences read successfully
Run-time error
Lseq and Locs disagree
..now exiting to system...

Now I checked the mailing list of LDHAT for the same problem, but couldn't come up with any solution. My question now is, do I have to use the sites.txt file that was created using the convert command for the test for recombination? I tried it and then the pairwise command works,but I am not sure if this is the right way to do it?

Any thoughts on this?

Thanks

[ch_at]

Sorry, my bad. It actually says in the manual that the sites.txt and locs.txt created with the convert command are then used as input for the pairwise testing for recombination. I must have read the manual 100 times and totally missed that one sentence.