Where Can I Find A Sliding Window Program For Sequence Diversity And Selection Analysis?

Question

[Joseph Hughes]

I am looking for a sliding window program or server like "SWAN: sliding window analysis of nucleotide sequence variability" or "SWAPSC: sliding window analysis procedure to detect selective constraints.". I still haven't had an answer from the authors so I am hoping someone on BioStar might be able to help.

[Pierre Lindenbaum]

you've already asked 4 questions on biostar. Please validate the answers.

[Casey Bergman]

what kind of selection analysis are you interested in?

Answer 1

[Casey Bergman]

Try Variscan for large-scale sliding window analysis of sequence diversity:

VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome-scale. The software, i) allows estimating a number of population genetic parameters; ii) conducts the analysis by using the sliding window or a wavelet transform-based methods to capture relevant information from DNA polymorphism data; iii) permits the visualization of the results by commonly used genome browsers...All of analyses implemented in VariScan can be conducted using the standard sliding window method that, in turn, can be used to obtain a graphical representation of the results (a detailed description is included in the appendix).