How can I filter ASVs by similarity during alignment, in prep for placement into a phylogenetic tree

[ovon]

Many years ago, I used to use QIIME 1 with pynast to filter ASV sequence sets prior to EPA placement with RAxML (now I would use epa-ng), and I'm looking for a practical way to do this now that both these pieces of software have gone by the wayside. I don't think I can get this pipeline running on a contemporary machine.

inputs: a set of ASVs that are pre-filtered based on interest, guide alignments and trees for specific clades, again selected based on interest

caveats: assume that we don't know a priori which ASVs fall w/in which clade, and are looking for a practical way to filter the set of ASVs prior to alignment and placement w/in each clade of interest. I'd like to do this for 8+ clades and two genes, so a smooth approach that isn't too hacky or labour intensive would be ideal

goals: given the input ASVs, align them to a template alignment based on similarity (i.e. dissimilar sequences are discarded during the alignment process) and use the resulting alignment to place the ASVs into a guide tree

does anyone have a working method for doing this? specifically: i don't know a good piece of software to use for discarding dissimilar ASVs when aligning to a template. tree placement is trivial once i have the correct inputs for that step

thanks in advance