I want to concatenate multiple protein coding gene (PCGs) sequences of an organism and calculate base composition at each codon position of concatenated PCGs in MEGA 6.0. Which software/ tool can i use for concatenation? Also how can i remove stop codons from the concatenated file in MEGA software to calculate base composition?
SequenceMatrix is recommend to concatenate multi-gene sequences.
Download SequenceMatrix:
https://github.com/gaurav/taxondna/releases/tag/1.8
SequenceMatrix software does more than just concatenate the genes, it also keeps track or reading frame for the protein-coding genes and has other useful features.
http://www.kmeverson.org/blog/easiest-way-to-concatenate-multiple-loci-into-a-single-nexus-file
I recommend watching this 5 minute tutorial/explanation video, to see if you think the SequenceMatrix tool suits your needs:
https://www.youtube.com/watch?v=Adwr-CZdNOM
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