Estimate a phylogenetic tree

We use the piq_build_tree app to build phylogenies. For this simple case, we will build a single phylogeny using the GTR model on one alignment. We have a utility script for this documentation that provides the local path to that data. We will then load that data and, as it contains quite a few sequences, we will use a subset of it. We use methods on the cogent3 object to do that.

In [1]:

import cogent3

from piqtree import download_dataset

aln_path = download_dataset("example.phy.gz", dest_dir="data")
aln = cogent3.load_aligned_seqs(aln_path, moltype="dna", format_name="phylip")
aln

import cogent3 from piqtree import download_dataset aln_path = download_dataset("example.phy.gz", dest_dir="data") aln = cogent3.load_aligned_seqs(aln_path, moltype="dna", format_name="phylip") aln

Out[1]:

	0
Bird	CTACCACACCCCAGGACTCAGCAGTAATTAACCTTAAGCATAAGTGTAACTTGACTTAGC
LngfishAu	..C.............AC.......G......A..G........C.A.G.......C...
LngfishSA	.A..............AA.............T....G.........A........C...T
LngfishAf	.A...............A.............AA..GGA................TCC...
Frog	AA.TTTGGT..TGT..T........G..A...A..G.A...G..C.A.G..C..T.C..T
Turtle	..T......................G..A..AA...........C.A.G..........T
Sphenodon	..C..............A.......G.....TA.............A............T
Lizard	..T........A...CA........G..A...A...........C.A.G..........T
Crocodile	..C............C.A........G....TA...G.......C.A.G.C....C...T
Human	................AA.......G.........T.......AC.A.GT..A...A...

17 x 1998 (truncated to 10 x 60) dna alignment

We now take a look at the help for the piq_build_tree app.

In [2]:

from cogent3 import app_help

app_help("piq_build_tree")

from cogent3 import app_help app_help("piq_build_tree")

Options for making the app
--------------------------
piq_build_tree_app = get_app(
    'piq_build_tree',
    model: piqtree.model._model.Model | str,
    rand_seed=None,
    bootstrap_reps=None,
    num_threads=None,
    other_options='',
)

Reconstruct a phylogenetic tree.

Given a sequence alignment, uses IQ-TREE to reconstruct a phylogenetic tree.

Parameters
----------
aln : Alignment
    The sequence alignment.
model : Model | str
    The substitution model with base frequencies and rate heterogeneity.
rand_seed : int | None, optional
    The random seed - None means no seed is used, by default None.
bootstrap_replicates : int | None, optional
    The number of bootstrap replicates to perform, by default None.
    If 0 is provided, then no bootstrapping is performed.
    At least 1000 is required to perform bootstrapping.
num_threads: int | None, optional
    Number of threads for IQ-TREE to use, by default None (single-threaded).
    If 0 is specified, IQ-TREE attempts to find the optimal number of threads.
other_options: str, optional
    Additional command line options for IQ-TREE.

Returns
-------
PhyloNode
    The IQ-TREE maximum likelihood tree from the given alignment.

Input type
----------
Alignment

Output type
-----------
PhyloNode

We build an app for estimating phylogenies with a GTR model

In [3]:

from cogent3 import get_app

phylo_gtr = get_app("piq_build_tree", model="GTR", bootstrap_reps=1000)
phylo_gtr

from cogent3 import get_app phylo_gtr = get_app("piq_build_tree", model="GTR", bootstrap_reps=1000) phylo_gtr

Out[3]:

piq_build_tree(model='GTR', rand_seed=None, bootstrap_reps=1000,
num_threads=None, other_options='')

Run the phylogeny estimation and display branches with support < 90%.¶

In [4]:

tree = phylo_gtr(aln)
dnd = tree.get_figure(show_support=True, threshold=90)
dnd.show(width=600, height=600)

tree = phylo_gtr(aln) dnd = tree.get_figure(show_support=True, threshold=90) dnd.show(width=600, height=600)