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No, but you can build your own using the
You would need to do codon modelling, i.e. constructing a likelihood function. It's quite trivial to do a sliding window type analysis (the An alternate would be to employ a Phylo-HMM. It is possible to apply that approach to an arbitrary parameter, including |
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Hello - firstly I'd just like to say I am really enjoying using this set of tools for analysing my sequence data. Thanks very much for putting this together.
I would like to calculate Tajima's D for my set of sequences and wondered if this was possible using Cogent3? I couldn't find this in the available statistical models. If possible I would like to obtain all pairwise comparisons.
I'm also interested in calculating the dN/dS ratio per codon along a sequence. There is a program written in R which does this (called OmegaMap) but it struggles with large datasets. I wondered if this was something that could be developed for Cogent3 (might be quite computationally challenging though) so no problem if not possible. This kind of analysis would allow codons under immune selection (or other) to be detected.
Many thanks
Odile
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