phylogenetics treats N's and gaps the same, so it seems sensible to treat them the same for alignment filtering too. Even though in principle they represent different things (Ns = sites we couldn't seuqence but know to be there, gaps=indels), the phylogenetic inference will treat them all as N's, so we should also treat them equally.
roblanf
commented
4 years ago
phylogenetics treats N's and gaps the same, so it seems sensible to treat them the same for alignment filtering too. Even though in principle they represent different things (Ns = sites we couldn't seuqence but know to be there, gaps=indels), the phylogenetic inference will treat them all as N's, so we should also treat them equally.