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 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 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