Hi,
I am using Tajima's D to identify signatures of selection across a chromosome with a sliding window analysis. I am looking for a coalescence simulation tool that will allow me to estimate p-values for the Tajima's D estimates across the chromosome while also correcting for type II error (false positives).
The chromosome I am investigating is approximately 19 million nucleotides in length. So far, I have investigated it using windows of 5, 50 and 500 KB in steps of 2.5, 25 and 250KB respectively.
To find the critical values of Tajima's D for these windows (to see if any chromosome regions show significant departures from neutral expectations), I have tried using Ardell's (20004) program SCANMS in conjunction with Hudson's (2002) program MS. This program combination takes far too long for the chromosome in question (in fact, the program has never finished even when run for a whole day).
Does anyone know if it is possible to program MS + SCANMS so that it can process a list of smaller chromosomal windows rather than one window at a time? If so, I might be able to analyze the different parts of the chromosome separately.
Regards,
gwilymh
I am using Tajima's D to identify signatures of selection across a chromosome with a sliding window analysis. I am looking for a coalescence simulation tool that will allow me to estimate p-values for the Tajima's D estimates across the chromosome while also correcting for type II error (false positives).
The chromosome I am investigating is approximately 19 million nucleotides in length. So far, I have investigated it using windows of 5, 50 and 500 KB in steps of 2.5, 25 and 250KB respectively.
To find the critical values of Tajima's D for these windows (to see if any chromosome regions show significant departures from neutral expectations), I have tried using Ardell's (20004) program SCANMS in conjunction with Hudson's (2002) program MS. This program combination takes far too long for the chromosome in question (in fact, the program has never finished even when run for a whole day).
Does anyone know if it is possible to program MS + SCANMS so that it can process a list of smaller chromosomal windows rather than one window at a time? If so, I might be able to analyze the different parts of the chromosome separately.
Regards,
gwilymh