I am new to bioinformatics. So if these questions seem you to a bit childish please forgive me.
I have two queries.
I am intending to perform a codon usage analysis followed by correspondence analyses for multiple microbial whole genomes of one bacterial species to find the association with the isolation source and ST type. Is this the right approach?
I have concatenated all the CDS in a single genome and joined all the genomes (average genes per genome is 4100). The problem is all the CDS when concatenated also have the stop codons in it. CodonW, famous for this analyses, cannot begin the analyses in the presence of stop codons. How can I remove stop codons?
Kindly suggest me a solution to the problem and concept.