Another variant of the question is: When should you not use Clustal or MUSCLE in DNA sequence alignment.
I am working on the 16S rRNA region of freshwater crabs (one family). I currently have 21 samples being aligned, which are around 500 bp each. I am constructing phylogenetic trees (NJ, MP and ML) along with chosen outgroup/s from ncbi.
Your help will be greatly appreciated.
Dear Dianne,
Using of the best sequence alignment tools depends sequence lengths, if your samples are quite different sequence lengths the MUSCLE will perform better than Clustal W.
I suggest to read this file:
http://biochem218.stanford.edu/Projects%202008/Sutton2008.pdf
Hi Sir Parviz Heidari,
Thank you for sharing this file. I've understood the criteria for choosing one method over the other. A very good read.
Thank you for your time, Sir.
Thank you Dianne for asking this question and Sir Parviz for your resourcefulness. I had the same query and the paper was useful for clarification.
Hi! I couldnt ope this link http://biochem218.stanford.edu/Projects%202008/Sutton2008.pdf
Sir, ould you send to me the link please?
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