GavinHuttley

# code from this piqtree issue https://github.com/iqtree/piqtree/issues/392
import cogent3 as c3

aln = c3.get_dataset("brca1")

# piqtree requires 3 sequences for a tree fit, so select an outgroup
outgroup = "Wombat"
# You need to write a loop that iterates all name pairs aside from the outgroup, use `for ingroups in itertools.combinations([n for n in aln.names if n != outgroup], 2):...`
# then in the loop
ingroups = ["Human", "Mouse"]

GavinHuttley

import os
from pathlib import Path
import tarfile

import cogent3
from cogent3.core.alignment import Alignment

COMPRESSED_DATA = Path("turtle_dataset.tar.gz")
TURTLE_PATH = Path("turtle_dataset/turtle.nex")
PARTITION_PATH = Path("turtle_dataset/partition.nex")