omicverse.alignment.build_phylogeny

omicverse.alignment.build_phylogeny(asvs_fasta, workdir=None, *, mafft_mode='auto', fasttree_model='gtr', gamma=True, mafft_threads=4, fasttree_threads=None, overwrite=False)

Build a phylogenetic tree end-to-end.

Returns {"aligned": ..., "tree": ..., "newick": "<tree-text>", ...}. The newick string has had vsearch’s ;size=N annotations stripped so that ete3 / unifrac can parse tip labels directly.

Return type:

Dict[str, str]