masked missing positions

[TCHeaven]

I am running a multiple sequence alignment with DNA data, in my input fasta file some sequences contain 'N's at positions with missing data. How will raxml-ng handle this? Do I need to exclude these samples with missing data from the analysis?

[amkozlov]

Well raxml-ng will treat Ns as missing data, so you don;t have to exclude such samples because of raxml-ng.

Of course, you might still want to exclude some samples with "too much" missing data based on your filtering strategy.