Hi, I am trying to align two protein sequences using MEGA so that I can then use the alignment for homology modelling. This is a new area to me however a bit of reading tells me that a good alignment is key to generating a good structural model and therefore I want to make sure that my alignment is as good as feasibly possible. My problem is as follows, once I have loaded the sequences I am able to align them using Clustal or Muscle. However, when I try and run the "Find best DNA/Protein model" function it says that a minimum of 3 taxa are required. Obviously as I am only do a pairwise alignment I only have 2 sequences and therefore cannot possibly have 3 taxa. My question is, is there a way to find out the best alignment settings for pairwise alignment using MEGA and if not has anyone got any advice on the best way to do this? Thanks in advance.
two sequences= Alignment pairwis (by blast)
Best exemple: https://blast.ncbi.nlm.nih.gov/
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Abbie Wright
It's not the problem of alignment but of phylogenetics.
As you also mention that you are doing a pairwise alignment, the two sequences cannot be represented in a tree (or better to say in a meaningful way). As they will be always 100 % related to each other in a tree. The question here is, why would someone construct a phylogenetic tree of just two sequences?
You will get this error in any software you use for the selection of the best-fit model.
You are doing a homology modelling, so it is not any restriction to not use more than two sequences. However, it is recommended to use as many sequences you can use to make a good tree.
Well the best method is to use BioEDIT before Mega. Align your sequence with the help of BioEDIT and use those sequences in MeGA for whatever analysis.
For all who are suggesting what alternative software can be used other than MEGA, please read and understand the question. It is not a software-related related problem.
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