I'm struggling to compute statistical significance and convergence in phylogeny. This will support my computed phylogenetic distances. I have used DECIPHER algorithm.
Phylogenetic distances are tuff on R.
I made a package for my case, as nothing existed. What is your personal case? maybe I could help… What kind of marker are you using?
Firstly, queries are aa seqs (Enzyme to be more specific), so the variation in the active site will be my marker. If you could send me the git_link of your package I'll try my luck. DECIPHER is an independent package, you can do almost everything with it, but it is not that versatile when it comes to AAstringset.
Well my package is dealing with dominant markers, but if you want to see if any function might be helpful : https://github.com/giby/Linarius/
there are a lot of protein specific computation… Try to get a ppt of a class about it… from last time I delt with it, I remember about blossum…
Thanks..!! I'll go through it.
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