Chloroplast genome phylogenetic analysis

Question

[a.bibek52]

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.