How to use DnaSP for polymorphye and SNP analyse in complete chloroplast genome sequences?

Question

[laisuliang]

Hello all!

I am using the DnaSP v5 to analyse the whole chloroplast genome sequences of two close related species and have two questions here:

1. I downloaded the chloroplast genomes sequence as .gb files, and then aligned and saved as NEXUS format file to import to DnaSP. The NEXUS file discarded all genes or CDSs annotations, so I have to assign ~110 coding regions one by one. It is a very time-consuming job. So, are there any useful tools to finish this job?

   For example, a software that can transfer the .gb files' genes or CDSs information to the NEXUS file.

   1. How to define the coding regions order (Forward or reverse) in DnaSP?