First you must group the sequences in concordance with species or populations that you want to compare.

 Thank you Juan, i have grouped the sequences according to their species, please how do i then calculate the intra and interspecific distance so as to estimate the barcoding gap.

thanks.

Many thanks Nikolaos & Dao L. Maba, that was quite helpful

you have to read the manual perfectly 

When you finish the alignment (ClustalW), click the pair distance bottom. That give you a matrix of the divergence (distance) of each of the sequences.

Dear All,

What is the best substitution model for calculating genetic distances? Could anyone explain me how to select that model, please.

Use all the substitution models and watch the changes in the phylogenetic trees.

Thank you. Ceda

How to make the histograms of the destribution of intraspecific and interspecific divergence distances to study the barcoding gap