Hi guys,
I have a certain protein of interest that I'm studying, I've already done some sequence and structure analysis using tools like Jackhmmer, HHpred, Blast, Pymol, etc. And now I'd like to try a phylogenetic analysis, to see what other proteins it looks like and what protein family it might be a part of. I've read works where researchers collect other homologous proteins and manage to assemble a phylogenetic tree and divide it into groups, I thought about doing something similar. Can anyone tell me any pipeline, book, or material that I can delve into before trying?
(I'm relatively new to bioinformatics, but would appreciate any help)
Dear Andre,
For designing a phylogenetic tree you can use MEGA X (any version) which is quite easy and reliable.
Instead, there are also available a number of online tools like 'Phylogeny fr' and many more, but I prefer to use MEGA!
If there is any need any help, let me know.
Thanks!
Thanks Asif Khan !
I tried to use MEGA, but its a bit slower. And, my data is something around 100.000 sequences of proteins. Then I'm using now some command line tools and trying to treat the data with some strategies.
The online tools has some problems, like the maximum of 4000 proteins to analyze in some cases, and others.
But, now I think I will do it in the next days, using a new strategy with help of a friend in my lab.
Again, thanks for your answer.
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