Pairwise JC distances

We estimate pairwise distances via the Jukes-Cantor model with the piq_jc_distances app.

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")

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")

We get help on the piqtree_jc_dist app.

In [2]:

cogent3.app_help("piq_jc_distances")

cogent3.app_help("piq_jc_distances")

Options for making the app
--------------------------
piq_jc_distances_app = get_app('piq_jc_distances', num_threads=None)

Compute pairwise JC distances for a given alignment.

Parameters
----------
aln : Alignment
    The alignment to compute pairwise JC distances for.
num_threads: int | None, optional
    Number of threads for IQ-TREE to use,
    by default None (uses all available threads).

Returns
-------
DistanceMatrix
    Pairwise JC distance matrix.

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

Output type
-----------
DistanceMatrix

Make an app and apply it to the alignment.

In [3]:

jc_dists = cogent3.get_app("piq_jc_distances")
dists = jc_dists(aln)
dists

jc_dists = cogent3.get_app("piq_jc_distances") dists = jc_dists(aln) dists

Out[3]:

names	Bird	Cow	Crocodile	Frog	Human	Lizard	LngfishAf	LngfishAu	LngfishSA	Mouse	Opossum	Platypus	Rat	Seal	Sphenodon	Turtle	Whale
Bird	0.0000	0.3828	0.3143	0.4059	0.3836	0.3656	0.4204	0.4122	0.3954	0.4134	0.3803	0.3886	0.4074	0.3753	0.3598	0.3139	0.3845
Cow	0.3828	0.0000	0.4085	0.3682	0.2100	0.3932	0.4143	0.3750	0.4048	0.2247	0.2397	0.2693	0.2302	0.1545	0.3778	0.3293	0.1460
Crocodile	0.3143	0.4085	0.0000	0.4280	0.4163	0.3968	0.4448	0.4186	0.4171	0.4475	0.4295	0.4154	0.4439	0.4102	0.3746	0.3396	0.4357
Frog	0.4059	0.3682	0.4280	0.0000	0.3940	0.4150	0.3504	0.2975	0.3520	0.3948	0.3673	0.3864	0.3982	0.3682	0.4349	0.3613	0.3805
Human	0.3836	0.2100	0.4163	0.3940	0.0000	0.3949	0.4390	0.3825	0.4160	0.2544	0.2889	0.3075	0.2586	0.2100	0.3895	0.3522	0.2214
Lizard	0.3656	0.3932	0.3968	0.4150	0.3949	0.0000	0.4524	0.4127	0.4165	0.3847	0.3780	0.4043	0.4156	0.3814	0.3714	0.3427	0.4078
LngfishAf	0.4204	0.4143	0.4448	0.3504	0.4390	0.4524	0.0000	0.2833	0.2384	0.4160	0.3878	0.4204	0.4435	0.4065	0.4408	0.3883	0.4082
LngfishAu	0.4122	0.3750	0.4186	0.2975	0.3825	0.4127	0.2833	0.0000	0.2877	0.3841	0.3883	0.3993	0.3850	0.3514	0.4131	0.3681	0.3692
LngfishSA	0.3954	0.4048	0.4171	0.3520	0.4160	0.4165	0.2384	0.2877	0.0000	0.3962	0.3647	0.4065	0.4248	0.3895	0.4230	0.3976	0.4048
Mouse	0.4134	0.2247	0.4475	0.3948	0.2544	0.3847	0.4160	0.3841	0.3962	0.0000	0.2425	0.2794	0.1226	0.2054	0.3811	0.3348	0.2315
Opossum	0.3803	0.2397	0.4295	0.3673	0.2889	0.3780	0.3878	0.3883	0.3647	0.2425	0.0000	0.2363	0.2721	0.2425	0.3696	0.3403	0.2488
Platypus	0.3886	0.2693	0.4154	0.3864	0.3075	0.4043	0.4204	0.3993	0.4065	0.2794	0.2363	0.0000	0.2918	0.2600	0.4031	0.3522	0.2671
Rat	0.4074	0.2302	0.4439	0.3982	0.2586	0.4156	0.4435	0.3850	0.4248	0.1226	0.2721	0.2918	0.0000	0.2234	0.4065	0.3530	0.2474
Seal	0.3753	0.1545	0.4102	0.3682	0.2100	0.3814	0.4065	0.3514	0.3895	0.2054	0.2425	0.2600	0.2234	0.0000	0.3811	0.3301	0.1688
Sphenodon	0.3598	0.3778	0.3746	0.4349	0.3895	0.3714	0.4408	0.4131	0.4230	0.3811	0.3696	0.4031	0.4065	0.3811	0.0000	0.3309	0.3820
Turtle	0.3139	0.3293	0.3396	0.3613	0.3522	0.3427	0.3883	0.3681	0.3976	0.3348	0.3403	0.3522	0.3530	0.3301	0.3309	0.0000	0.3356
Whale	0.3845	0.1460	0.4357	0.3805	0.2214	0.4078	0.4082	0.3692	0.4048	0.2315	0.2488	0.2671	0.2474	0.1688	0.3820	0.3356	0.0000