Dear Sergei,
I want to know if I can calculate the exact dN/dS ratio between different aligned sequences in Hyphy. Assuming I have 9 aligned sequences from different isolates of a virus and I want to know dN/dS ratio between each two sequence.

Dear Davoodi,

Your question can be answered in several different ways, depending on what your ultimate objective is. For example, do you wish to compute pairwise dN/dS (i.e. ignore the phylogenetic structure), or if you want to estimate dN/dS at each branch of the tree relating your nine sequences?

Please be more specific, and I'll try to point you in the right direction.

Cheers,
Sergei

Dear Sergei, following my previous question it is nesessary to say that my main aim is to compute dN/dS ratio for each 2 sequences ignoring phylogenetic structure.
best regards,
Davoodi

Dear Davoodi,

Try running the standard analysis (located under the 'Analysis->Standard Analyses' menu) Phylohandbook.bf, located in the Miscellaneous rubrik. Select the dSdN.bf option when prompted. This analysis allows you to compute dS and dN between all pairs of sequences in an alignment both using the phylogeny and pairwise, which is useful for comparison to see if ignoring the phylogenetic structure makes the estimates substantially different. The analysis still requires a tree, which you can easily build for your sequences (e.g. using neighbor joining, or a likelihood heuristic).

Cheers,
Sergei

Dear Sergei,
soorry to bother you again.
i tried to run Phylohandbook.bf, but this option dos'nt work. after running this option I recieve an error message like this:
<current BL command:,<doctype html public--//w3c//d current task has been terminated.>
all other options work well.
I don't know what i have to do? it is nessesary to say  I use a windows version of hyphy.
thank you very much.
Davoodi

Dear Davoodi,

I don't quite understand what is causing the error (seems like it's an http related issue). You can download the batch file from this link Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login and run it from HyPhy by choosing File>Open>Open Batch File command.

Cheers,
Sergei

Dear Sergei,
I want to thank you for giving me the best answer. Thank you.
here I have another request. you mentioned elsewhere that you have just finished a book chapter on selection analysis. would you mind sending me the draft version of this chopter.
sincerely:
davoodi
davoodia@yahoo.com