Inferring Ancestral Protein Sequences Using Mega
Is it possible to infer full ancestral protein sequences using MEGA? The reason I ask is that it seems like the only input to their ancestral reconstruction program is a newick tree, and not an MSA. Without knowing the actual sequences, I don't understand how it is possible to do any sort of reconstruction. If anybody has experience with this I would appreciate your feedback.
1 answer
Yes, you're right, as with only a NEWICK tree, you can't predict ancestral states. Honestly, I hate using MEGA and would avoid using the program at all costs. I don't understand why anyone uses it, but, that's my opinion.
You can infer ancestral states using MESQUITE.
Log in to answer this question.
More posts like this
-
Ancestral sequence reconstruction at each node of a gene tree
written by biomonte
-
Issue with FastML Ancestral Sequence Reconstruction
written by CM •
-
Plot phylogenetic tree with all ancestor nodes
written by AfinaM •
-
Input arguments to list ancestral sequences in emboss phylip (dnapars)
written by shpak.max •
-
Export phylogenetic tree from "official" trees available on internet
written by erica.fary •
-
Infer ancestral sequence from a Multiple Sequence Alignment
written by anuragm
-
Doubts regarding phylogeny analysis with protein sequence
written by lia.elias •
-
Encountering Paml Error When Using Lazarus Package
written by Ncemami •
-
Which Phylogeny Software Should I Used To View Tree Of 5000 Sequences?
written by Sagar Nikam
-
Is There Any Guide For Species Tree Reconstruction?
written by Robert Jenkins •
