Mr. FAM,

You can use MEGA7 software package for smarter extraction and alignment of fasta files from NCBI genebank. Trimming of sequence is also possible.

Olá Fabio, your current plan of downloading complete genomes, then get the mitogenomes, and then select whatever DNA segments you are interested in via trimming might work well and should not be as painful as it sounds if you use Geneious. I know you are searching for a free-of-charge option, but I anyway wanted to let you know that this program would make your task relatively easy (WAY easier than in Mesquite, MEGA, etc).  Also, a couple of days ago I saw that  a new R package was released and, I think,it  does exactly what you want to do. I will confirm this info and get its name and let you know. 

Found it: "AnnotationBustR: An R package to extract subsequences from GenBank annotations" Here: https://peerj.com/preprints/2920.pdf  

Eliecer, thanks!

I've heard of Geneious, but unfortunately I am, at the present moment, without fundings to acquire it. So free softwares will have to do. I will check O'Meara's package. It looks like the thing for me now.

You are welcome, Fabio! Good luck on the task. Abraços.

It did the trick wonderfully! However, it uses genbank annotations to find the genes and extract them. That left me with only one genome that will have to be processed "by hand". In anyway, it was very helpful.

Saludos!

It did the trick wonderfully! However, it uses genbank annotations to find the genes and extract them. That left me with only one genome that will have to be processed "by hand". In anyway, it was very helpful.

Saludos!