Construct a maximum likelihood phylogenetic tree

A maximum-likelihood phylogenetic tree can be constructed from cogent3 alignment objects using build_tree.

Usage

Basic Usage

Construct a cogent3 alignment object, then construct a maximum-likelihood tree.

from cogent3 import load_aligned_seqs
from piqtree import build_tree

aln = load_aligned_seqs("my_alignment.fasta", moltype="dna")

tree = build_tree(aln, "GTR")
log_likelihood = tree.params["lnL"]

Ultrafast Bootstrap

To perform ultrafast bootstrapping, the number of replicates can be specified. The number of replicates must be at least 1000. The support for each node in the tree object can be accessed from node.support.

from cogent3 import load_aligned_seqs
from piqtree import build_tree

aln = load_aligned_seqs("my_alignment.fasta", moltype="dna")
tree = build_tree(aln, "K81+FO", bootstrap_replicates=2000)

Reproducible Results

For reproducible results, a random seed may be specified.

Caution: 0 is a specific random seed. None is equivalent to no random seed being specified.

from cogent3 import load_aligned_seqs
from piqtree import build_tree

aln = load_aligned_seqs("my_protein.fasta", moltype="protein")

tree = build_tree(aln, "Dayhoff", rand_seed=3)

Multithreading

To speed up computation, the number of threads to be used may be specified. By default, the computation is done on a single thread. If 0 is specified, then IQ-TREE attempts to determine the optimal number of threads.

Caution: If 0 is specified with small datasets, the time to determine the optimal number of threads may exceed the time to find the maximum likelihood tree.

from cogent3 import load_aligned_seqs
from piqtree import build_tree

aln = load_aligned_seqs("my_alignment.fasta", moltype="dna")
model = "HKY+I+G6"

tree = build_tree(aln, model, num_threads=4)

Additional options

Additional options in the format that would be passed to the IQ-TREE CLI can be set. Options in other_options already allowed through build_tree will be ignored.

from cogent3 import load_aligned_seqs
from piqtree import build_tree

aln = load_aligned_seqs("my_alignment.fasta", moltype="dna")

tree = build_tree(aln, "GTR", other_options="--epsilon 0.1 -n 0")