taxodist 0.4.0

Taxonomic Distance and Phylogenetic Lineage Computation

taxodist

Taxonomic distance and phylogenetic lineage computation for any taxon on Earth.

taxodist retrieves full hierarchical lineages from The Taxonomicon and computes a tree metric distance between any two taxa: a pair of dinosaurs, a dinosaur and a fungus, two species of fly, or an oak tree and a human.

Installation

pip install taxodist

pip install git+https://github.com/rodrigosqrt3/taxodist-py.git

Basic usage

from taxodist import (
    get_lineage, taxo_distance, mrca, distance_matrix, 
    filter_clade, taxo_path, save_cache, load_cache
)

# Get a full lineage
get_lineage("Tyrannosaurus")

# Distance between two taxa
taxo_distance("Tyrannosaurus", "Velociraptor")

# Most recent common ancestor
mrca("Tyrannosaurus", "Triceratops")   # "Dinosauria"
mrca("Tyrannosaurus", "Homo")          # "Amniota"

# Pairwise distance matrix
theropods = ["Tyrannosaurus", "Velociraptor", "Spinosaurus", "Allosaurus"]
distance_matrix(theropods)

# Filter taxa by clade
taxa =["Tyrannosaurus", "Triceratops", "Homo", "Quercus"]
filter_clade(taxa, "Dinosauria")

# Get the path between two taxa
taxo_path("Tyrannosaurus", "Velociraptor")

# Save and restore the lineage cache across sessions
save_cache("my_cache.pkl")
load_cache("my_cache.pkl")