This crate aims to be a general purpose package to deal with phylogenetic trees and simulate them. Is also comes with a simple CLI tool to manipulate and simulate phylogenetic trees directly from the command line.
phylotreeTo use this crate just run cargo add phylotree in your cargo project or add phylotree = "0.1.2" to your Cargo.toml file.
To install the CLI you can use
cargo install phylotree
Or you can build the project from source:
shell
git clone https://github.com/lucblassel/phylotree.git
cd phylotree
cargo build --release
mv target/release/phylotree <somewhere/in/your/PATH>
Below is some sample usage of the phylotree crate, please see docs.rs/phylotree for the full documentation.
```rust use phylotree::tree::Tree;
////////////////////////////////// // Building a tree from scratch // ////////////////////////////////// let mut tree = Tree::new();
// Add the root node let root = tree.add(Node::new());
// Add a child to the root let child1 = tree.addchild(Node::newnamed("Child1"), root, None).unwrap(); // Add a child to the root with a branch length let child2 = tree.addchild(Node::newnamed("Child2"), root, Some(0.5)).unwrap();
// Add more children let child3 = tree.addchild(Node::newnamed("Child_3"), child1, None).unwrap();
// Get depth of child asserteq!(tree.get(&child3).unwrap().getdepth(), 2)
/////////////////////////////// // Reading and writing trees // /////////////////////////////// let newickstr = "((A:0.1,B:0.2)F:0.6,(C:0.3,D:0.4)E:0.5)G;"; let tree = Tree::fromnewick(newick_str).unwrap();
asserteq!(tree.tonewick().unwrap(), newick_string)
////////////////////// // Traversing trees // ////////////////////// let newickstr = "((A,B)C,(D,E)F)G;"; let mut tree = Tree::fromnewick(newickstr).unwrap(); let root = tree.getroot().unwrap();
let preorder: Vec<_> = tree.preorder(&root).unwrap() .iter() .map(|nodeid| tree.get(nodeid).unwrap().name.clone().unwrap()) .collect();
assert_eq!(preorder, vec!["G", "C", "A", "B", "F", "D", "E"]);
///////////////////// // Comparing trees // /////////////////////
// The second tree is just a random rotation of the first, // they represent the same phylogeney let newickorig = "((A:0.1,B:0.2)F:0.6,(C:0.3,D:0.4)E:0.5)G;"; let newickrota = "((D:0.3,C:0.4)E:0.5,(B:0.2,A:0.1)F:0.6)G;";
let treeorig = Tree::fromnewick(newickorig).unwrap(); let treerota = Tree::fromnewick(newickrota).unwrap();
let rf = treeorig.robinsonfoulds(&tree_rota).unwrap();
assert_eq!(rf, 0)
///////////////////////////////// // Computing a distance matrix // ///////////////////////////////// let newick = "((T3:0.2,T1:0.2):0.3,(T2:0.4,T0:0.5):0.6);"; let tree = Tree::fromnewick(newick).unwrap(); // Compute the whole distance matrix let matrix = tree.distancematrix_recursive().unwrap(); let phylip="\ 4 T0 0 1.6 0.9 1.6 T1 1.6 0 1.5 0.4 T2 0.9 1.5 0 1.5 T3 1.6 0.4 1.5 0 ";
asserteq!(matrix.tophylip(true).unwrap(), phylip) ```
There is a simple CLI that comes with this package:
``` A simple command line tool to manipulate phylogenetic trees
Usage: phylotree
Commands: generate Generate random tree(s) stats Get statistics about a tree compare Compare two phylogenetic trees matrix Output the phylogenetic distance matrix of the tree distance Outputs a subset of phylogenetic distances collapse Collapse branches that are under a certain branch length threshold remove Remove tips from the trees deduplicate Remove or collapse branches corresponding to identical sequences in a reference alignment help Print this message or the help of the given subcommand(s)
Options: -h, --help Print help ```
A python package has also been implemented, using PyO3 to create the python bindings. It is available on PyPi, you can see the API of the package here.
Example usage:
```python from phylotree import Tree
tree = Tree.from_newick("path/to/tree.nwk")
tree = Tree.from_string("((A,(C,E)D)B,((H)I)G)F;")
tree.to_newick()
tree.nnodes() tree.ntips() tree.height() tree.diameter() tree.ncherries() tree.colless() tree.sackin() tree.isbinary tree.is_rooted
names = tree.getleafnames() info = tree.getnodeattributes(name=names[0]) print(f"Parent edge has length: {info['parentedge']}") distbranches, disttopo = tree.getdistance(names=(names[0], names[1]))
distancematrix = tree.tomatrix() distmat = distancematrix[(names[0], names[1])] assert distbranches == distmat
tree.compress() # Remove nodes with 1 parent and 1 child tree.rescale() # Change branch lengths tree.prune(name="D") # Remove sbutree rooted a specific node
for nodeid in tree.traversal(order="levelorder"): node = tree.getnodeattributes(id=nodeid) print(node.name) ```