swap IQ-TREE with piqtree? #1930
Description
Hi developers of the amazing nextstrain!
The developers of IQ-TREE have noted usage of the command-line iqtree application in your workflows and wanted to bring to your attention piqtree (you can get our preprint here). piqtree is a Python package that binds the IQ-TREE routines. There is a negligible difference in compute performance to the original tool. It integrates into Python with cogent3.
We wondered if you'd be interested in using piqtree instead? We think it will reduce your development burden.
I've taken a stab at that below by rewriting your build_iqtree() function. As you can see, it simplifies your code.
I'm happy to make this a formal PR if you'd like, but I thought I'd check here first.
# replacing the `build_iqtree` function with cogent3 alignment and tree objects and
# piqtree for the phylogeny estimation.
def build_iqtree(aln_file, out_file, substitution_model="GTR", nthreads=1, tree_builder_args=None):
"""
build tree using piqtree
arguments:
aln_file file name of input aligment
out_file file name to write tree to
"""
import cogent3 as c3
aln = c3.load_aligned_seqs(aln_file, moltype="dna")
# make sure the seq names won't cause problems with IQ-TREE algorithms
seqname_aliases = {n: f"s{i}" for i, n in enumerate(aln.names)}
rn_aln = aln.rename_seqs(lambda x: seqname_aliases[x])
build_tree = c3.get_app(
"piq_build_tree", model=substitution_model, num_threads=nthreads, other_options=tree_builder_args
)
tree = build_tree(rn_aln)
# revert back to the original sequence names
rn_tree = tree.renamed_nodes({a: n for n, a in seqname_aliases.items()})
rn_tree.write(out_file)
return rn_tree, aln.names