How to prep MAFFT alignment files for use in R packages ape and pegas?

Question

[juliuspasion1994]

Hello everyone,

I have a single alignment file that I would like to analyze using the Tajima's D test in pegas. The alignment file is in Clustal format, and was generated using MAFFT. Within my file, I have alignments for every gene in the reference genome, aligned to the rest of the genomes in the population I'm studying.

Is there any file processing I have to do in order to import the alignment file into R? I know I have to use the ape function DNAbin in order to use the Tajima's D test, but I'm not sure what needs to be done in terms of processing my alignment file to be ready for import.

If anyone could help, I would be very grateful!