H-mito includes a suite of scripts for mtDNA haplogrouping prediction based on the on the phylogenetic tree available on the PhyloTree.org website.
The main Python module will help you to extract mutation lists and the Clustal2package to join and align data.
As a user, you can find yourself in one of the following three situations:
· you already have the mutation list(s) for you sequence(s) · you only have the alignment of your sequence(s) to the reference · you only have the sequence(s)
In these cases you have to take the following actions, respectively: · just run h-mito (A). · first extract the mutation list(s) by using mitoP, then run h-mito (A+B). · first align your sequence(s) to the reference, then extract the mutation list(s), and finally run h-mito. Notice that, in this case, the alignment will be done automatically by clustalw2 and a visual check of it can be necessary (A+B+C).
