hey i'm not sure if when i do concatenate alignment for proteins of different species (for phylogenetics) should I use whole protein alignments (i think so) or alignments of protein domains (fragments).
best
Marcin
I guess this question is specific and should be decided by you according to your protein candidate/s. But the one thing I could recommend is, it would be more important to treat all the candidates/sequences in same way, so I think using whole protein or domain would not affect so much. I also think using whole protein can be more logical to include all the variations not just for specific domain.
Abhijeet Singh Thanks, I chose a few non-multidomain proteins of similar length common to each species :)
I agree with the previous answer. Given your choice of proteins (single domain proteins, similar lengths), I assume they are pretty conserved, so I'd say it's better to use the full length alignment because (1) it's unlikely to make a difference to use the fragments, and (2) you won't have to make the decision how to trim the full-length alignment to derive the fragments, which would need to be justified.
If you are looking for conserved sites in protein from same family or genus. Conserved Region allingmrnt is important. But I would say in principle MSA whole with proper constrains setup in allingmrnt input will give you same results.
I actually think it all depends on the question you want to answer. if you are looking for a phylogenetics tree that would be well supported, I recommend you use the whole protein seq. You might want to ensure that the proteins you chose have enough site information to generate a desired tree if the tree.
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