How to compute convergence in phylogeny in R?

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6.4 years ago

arpankbasak ▴ 10

I'm struggling to compute statistical significance and convergence in phylogeny. This will support my computed phylogenetic distances. I have used DECIPHER algorithm.

Phylogeny R Decipher • 1.3k views

ADD COMMENT • link updated 6.4 years ago by gbl1 ▴ 80 • written 6.4 years ago by arpankbasak ▴ 10

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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?

ADD REPLY • link 6.4 years ago by gbl1 ▴ 80

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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.

ADD REPLY • link 6.4 years ago by arpankbasak ▴ 10

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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…