The available piqtree apps

To see the apps that piqtree makes available, use the cogent3 function available_apps() as follows.

In [1]:

from cogent3 import available_apps

available_apps("piqtree")

from cogent3 import available_apps available_apps("piqtree")

Out[1]:

0 rows x 7 columns; unset columns=unset columns: 'package', 'name', 'composable', 'doc', 'input type', 'output type', 'licenses'

For a particular app, use the cogent3 function app_help() to find out what the options are.

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

In [3]:

from cogent3 import app_help

app_help("piq_fit_tree")

from cogent3 import app_help app_help("piq_fit_tree")

Options for making the app
--------------------------
piq_fit_tree_app = get_app(
    'piq_fit_tree',
    tree: cogent3.core.tree.PhyloNode,
    model: piqtree.model._model.Model | str,
    num_threads=None,
    other_options='',
    bl_fixed=False,
)

Fit branch lengths and likelihood for a tree.

Given a sequence alignment and a fixed topology,
uses IQ-TREE to fit branch lengths to the tree.

Parameters
----------
aln : Alignment
    The sequence alignment.
tree : PhyloNode
    The topology to fit branch lengths to.
model : Model | str
    The substitution model with base frequencies and rate heterogeneity.
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.
bl_fixed: bool, optional
    If True, evaluates likelihood using the provided branch lengths on the tree.
    Branch lengths will be treated as constant in this case, with any unspecified
    branch lengths still being optimised. Otherwise if False, branch lengths are
    fitted to the tree whether provided or not. By default False.
other_options: str, optional
    Additional command line options for IQ-TREE.

Returns
-------
PhyloNode
    A phylogenetic tree with the same given topology fitted with branch lengths.

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

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