Chloroplast genome phylogenetic analysis
Hello Biostars,
Can anybody help me to know whether I have to correct the direction (reverse complement) the Short Single Copy (SSC) region of the Chloroplast genome when I am doing Multiple Sequence Alignment (MSA) for the Phylogenetic inference? I have been trying to learn MSA and Phylogenetic tree for some of the available chloroplast genome of Arabidopsis sp. and found some sequences in the NCBI have a reverse complemented SSC region.
Thank you.
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