Phylo

Phylo a fast, extensible, general-purpose, and WebAssembly-capable library for phylogenetic analysis and inference written in Rust. Phylo-rs leverages a combination of memory safety, speed, and native WebAssembly support offered by Rust to provide a robust set of memory-efficient data structures with basic algorithms ranging from tree manipulation with SPR to computing tree statistics such as phylogenetic diversity.

A note on implementation

Implementation of tree-like structures in rust can be difficult and time-intensive. Additionally implementing tree traversals and operations on tree structures (recursive or otherwise) can be an even bigger task.

This crate aims to implement a majority of such methods as easily-derivable traits, so you don't have to implement them from scratch where they are not needed.

We also provide a struct so you don't have to implement one...

Using phylo

Most of the functionality is implemented in crate::tree::simple_rtree. The crate::tree::ops module is used to dealt with phylolgenetic analysis that require tree mutations such as SPR, NNI, etc. crate::tree::simulation module is used to simulate random trees crate::tree::io module is used to read trees from various encodings crate::tree::distances module is used to compute various types of distance between nodes in a tree and between trees crate::iter is a helper module to provide tree traversals and iterations.

Building trees

The simplest way to build a tree is to create an empty tree, add a root node and then add children to the various added nodes:

use phylo::prelude::*;

let mut tree = SimpleRootedTree::new(1);

let new_node = Node::new(2);
tree.add_child(tree.get_root_id(), new_node);
let new_node = Node::new(3);
tree.add_child(tree.get_root_id(), new_node);
let new_node: Node = Node::new(4);
tree.add_child(2, new_node);
let new_node: Node = Node::new(5);
tree.add_child(2, new_node);

Reading and writing trees

This library can build trees strings (or files) encoded in the newick format:

use phylo::prelude::*;

let input_str = String::from("((A:0.1,B:0.2),C:0.6);");
let tree = SimpleRootedTree::from_newick(input_str.as_bytes())?;

Traversing trees

Several traversals are implemented to visit nodes in a particular order. pre-order, post-order. A traversals returns an Iterator of either nodes or NodeID's in the order they are to be visited in.

use phylo::prelude::*;

let input_str = String::from("((A:0.1,B:0.2),C:0.6);");
let tree = SimpleRootedTree::from_newick(input_str.as_bytes())?;

let dfs_traversal = tree.dfs(tree.get_root_id()).into_iter();
let bfs_traversal = tree.bfs_ids(tree.get_root_id());
let postfix_traversal = tree.postord_ids(tree.get_root_id());

Comparing trees

A number of metrics taking into account topology and branch lenghts are implemented in order to compare trees with each other:

use phylo::prelude::*;

fn depth(tree: &SimpleRootedTree, node_id: usize) -> f32 {
    tree.depth(node_id) as f32
}

let newick_1 = "((A:0.1,B:0.2):0.6,(C:0.3,D:0.4):0.5);";
let newick_2 = "((D:0.3,C:0.4):0.5,(B:0.2,A:0.1):0.6);";

let tree_1 = SimpleRootedTree::from_newick(newick_1.as_bytes())?;
let tree_2 = SimpleRootedTree::from_newick(newick_2.as_bytes())?;

tree_1.precompute_constant_time_lca();
tree_2.precompute_constant_time_lca();

tree_1.set_zeta(depth);
tree_2.set_zeta(depth);


let rfs = tree_1.rfs(&tree_2);
let wrfs = tree_1.wrfs(&tree_2);
let ca = tree_1.ca(&tree_2);
let cophen = tree_1.cophen_dist_naive(&tree_2, 2);