Hi,
I'm currently trying to do a multiple sequence alignment for a gene family using the coding nucleotide sequences. I want to create an alignment based on the amino acid sequences but that is in the form of nucleotides, so that I'm able to account for synonymous mutations in my subsequent analyses. The ClustalW (codons) and MUSCLE (codons) alignment options in MEGA-X sound like they fit my needs. However, I am unable to select them in the drop down menu and they are greyed out (see picture attached).
Does anyone know of any reasons why these options might not be available to me?
Thanks in advance,
Jacob
First option: Have you tried translating your data from genome sequences to amino-acids? That may help MEGA to interpret the data as proteins.
Second option: When you open your file, MEGA "asks" if the sequences are protein-coding (and even asks the origin of them). Try saving your data as a new FASTA file and then opening like that in MEGA.
I hope any of both may help.
*Although I believe you may be able to align your data as genetic sequences, I do not know much of proteomics and what would be the adequate method (via ACTG or amino-acids) to perform a phylogenetic analysis with that specific objective.
Thank you Jose Alberto Lopez-Aleman , saving my data in FASTA format and then reopening in MEGA seems to have done the trick!
I have already used amino acid sequences, I am currently trying out a few different approaches until I reach a consensus that I am confident in...
Hi. The Mega6 version has less complexity and hassle than the MegaX. Given that it has a lower version, but does not diminish the credibility of your work.
Best.,
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