You may :
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Read, build, modify and displays as svg reconciled phylogenetic trees.
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Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconciliation levels
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Build a svg representation of a phylogenetic reconciled (or not) tree with events (loss, duplication, speciation, transfer).
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Read a recphyloxml file: create a svg representation of the gene tree(s) and the associated species tree.
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Read 2 nested recphyloxml files: create svg representations of the gene tree(s), the associated symbiot tree(s) and the associated species tree.
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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.
You may use the "thirdkind" software https://github.com/simonpenel/thirdkind/wiki based on 'light_phylogeny' to represent trees with 1, 2 or 3 reconciliation levels
Keywords: phylogeny, reconciled trees, phylogenetic trees
phyloXML, recPhyloXML, rooted newick (NHX tags will not be considered).
For output examples, please see the thirdkind home page https://github.com/simonpenel/thirdkind/wiki
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.");
}
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
Read and display a reconciled tree from a recPhyloXML file:
https://github.com/simonpenel/light_phylogeny/blob/master/examples/read_recphyloxml.rs
See Rust documentation : https://docs.rs/light_phylogeny/
https://github.com/simonpenel/thirdkind
See http://phylariane.univ-lyon1.fr/recphyloxml/
recPhyloXML paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198865/
phyloXML paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774328/
- Possible problem with the obsolete version of recPhyloXML format (speciationLoss is supported, speciationOutLoss and speciationOut are not supported yet)
"Arena" Tree structure is inspired by the code proposed here
