Read, build,modify and displays as svg and manipulates reconciled phylogenetic trees.
Trees must be rooted.
Build a svg representation of a phylogenetic reconciled (or not) tree with events (loss, duplication, speciation, transfer).
Read a recphyloxml file: create a svg representation of the gene tree(s) and the associated species tree.
Read a newick or phyloxml file: create a svg representation of the gene tree only.
You may use light_phylogeny functions and methods to build, manipulate, modify or draw phylogenetic trees.
Keywords: phylogeny, reconciled trees, phylogenetic trees
Formats:
phyloXML, recPhyloXML, rooted newick ( NHX balises will not be considered ).
Output examples
multiple genes reconciliation recphyloxml:
single gene reconciliation in recphyloxml:
the same gene reconciliation in phyloxml:
Using the API:
https://crates.io/crates/light_phylogeny
You may find code examples in the "examples" directory.
Simple Rust example: read a newick.txt file and creates the svg
use light_phylogeny::{ArenaTree,Options,Config,read_newick,phyloxml_processing};
fn main() {
let mut tree: ArenaTree<String> = ArenaTree::default();
let options: Options = Options::new();
let config: Config = Config::new();
read_newick("examples/newick.txt".to_string(), &mut tree);
phyloxml_processing(&mut tree, &options, &config,"read_newick-clado.svg".to_string());
println!("Please open output file 'read_newick-clado.svg' with your browser");
let mut tree: ArenaTree<String> = ArenaTree::default();
let mut options: Options = Options::new();
options.real_length_flag = true;
let config: Config = Config::new();
read_newick("examples/newick.txt".to_string(), &mut tree);
phyloxml_processing(&mut tree, &options, &config,"read_newick-real-clado.svg".to_string());
println!("Please open output file 'read_newick-real-clado.svg' with your browser");
}
Some newick examples are available here : https://github.com/simonpenel/light_phylogeny/tree/master/newick_examples
Simple Rust example:build a gene tree, creates the svg, modiy the tree and creates a new svg:
use light_phylogeny::{ArenaTree,Options,Config,Event,add_child,move_child,phyloxml_processing,
summary,reset_pos};
fn main() {
let mut tree: ArenaTree<String> = ArenaTree::default();
let mut options: Options = Options::new();
let config: Config = Config::new();
// Create a new node root
let root = tree.new_node("root".to_string());
// Create new nodes
let a1 = tree.new_node("a1".to_string());
let a2 = tree.new_node("a2".to_string());
let a = tree.new_node("a".to_string());
let b1 = tree.new_node("b1".to_string());
let b2 = tree.new_node("b2".to_string());
let b = tree.new_node("b".to_string());
let c = tree.new_node("c".to_string());
let d = tree.new_node("d".to_string());
println!("Initial tree :");
summary(&mut tree);
// Set names
tree.arena[root].name = "MyRoot".to_string();
tree.arena[a].name = "Gene A".to_string();
tree.arena[a1].name = "Gene A1".to_string();
tree.arena[a2].name = "Gene A2".to_string();
tree.arena[b].name = "Gene B".to_string();
tree.arena[b1].name = "Gene B1".to_string();
tree.arena[b2].name = "Gene B2".to_string();
tree.arena[c].name = "Gene C".to_string();
tree.arena[d].name = "Gene D".to_string();
println!("");
println!("Tree after name attribution:");
summary(&mut tree);
// Set hierarchy
// a1 and a2 are children of a
add_child(&mut tree,a,a1);
add_child(&mut tree,a,a2);
// a1 and a2 are children of a
add_child(&mut tree,b,b1);
add_child(&mut tree,b,b2);
// a and b are children of c
add_child(&mut tree,c,a);
add_child(&mut tree,c,b);
// c and d are children of root
add_child(&mut tree,root,c);
add_child(&mut tree,root,d);
println!("");
println!("Tree after hierarchy attribution:");
summary(&mut tree);
// Display internal nodes
options.gene_internal = true ;
phyloxml_processing(&mut tree, &options, &config,"modify_tree_ini.svg".to_string());
println!("Add a loss to C");
let loss = tree.new_node("loss".to_string());
tree.arena[loss].name = "Loss".to_string();
tree.arena[loss].e = Event::Loss;
add_child(&mut tree,c,loss);
println!("Add a node up to B");
let add = tree.new_node("add".to_string());
tree.arena[add].name = "Added up to B".to_string();
println!("Move A to new node ");
move_child(&mut tree, a, add);
println!("Move B to new node ");
move_child(&mut tree, b, add);
println!("Move new node to C ");
add_child(&mut tree, c, add);
println!("Tree after hierarchy modification:");
summary(&mut tree);
reset_pos(&mut tree);
phyloxml_processing(&mut tree, &options, &config,"modify_tree_mod.svg".to_string());
println!("Please open output files 'modify_tree_ini.svg' and 'modify_tree_mod.svg' with your browser");
println!("OK.");
}
Code Examples
You may try the codes in the 'examples' directory:
cargo run --example read_newick
cargo run --example build_tree
cargo run --example lca
cargo run --example modify_tree
Source documentation
See Rust documentation : https://docs.rs/light_phylogeny/
recPhyloXML documentation
See http://phylariane.univ-lyon1.fr/recphyloxml/
recPhyloXML paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198865/
phyloXML documentation
phyloXML paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774328/
Under development:
- Possible problem with the obsolete version of recPhyloXML format (speciationLoss is supported, speciationOutLoss and speciationOut are not supported yet)
Tree drawing algorithms and structures
"Arena" Tree structure is inspired by the code proposed here
Tree drawing algorithms are well explained here and here