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:

https://raw.githubusercontent.com/simonpenel/rectree2svg/9244f3136961f909fd7b33818f0a220e3f32c880/tree2svg.example.svg

single gene reconciliation in recphyloxml:

https://raw.githubusercontent.com/simonpenel/rectree2svg/9244f3136961f909fd7b33818f0a220e3f32c880/FAM000696reconciliatedrecphyloxml.svg

the same gene reconciliation in phyloxml:

https://raw.githubusercontent.com/simonpenel/rectree2svg/9244f3136961f909fd7b33818f0a220e3f32c880/FAM000696reconciliatedxml.svg

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 lightphylogeny::{ArenaTree,Options,Config,readnewick,phyloxml_processing};

fn main() { let mut tree: ArenaTree = ArenaTree::default(); let options: Options = Options::new(); let config: Config = Config::new(); readnewick("examples/newick.txt".tostring(), &mut tree); phyloxmlprocessing(&mut tree, &options, &config,"readnewick-clado.svg".tostring()); println!("Please open output file 'readnewick-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/lightphylogeny/tree/master/newickexamples

Simple Rust example: build a gene tree with a duplication and creates the svg ``` use lightphylogeny::{ArenaTree,Options,Config,Event,phyloxmlprocessing,summary}; fn main() { let mut tree: ArenaTree = 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 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[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
tree.arena[a1].parent = Some(a);
tree.arena[a2].parent = Some(a);
tree.arena[a].children.push(a1);
tree.arena[a].children.push(a2);
// a and b are children of c
tree.arena[a].parent = Some(c);
tree.arena[b].parent = Some(c);
tree.arena[c].children.push(a);
tree.arena[c].children.push(b);
// c and d are children of root
tree.arena[c].parent = Some(root);
tree.arena[d].parent = Some(root);
tree.arena[root].children.push(c);
tree.arena[root].children.push(d);
println!("");
println!("Tree after hierarchy attribution:");
summary(&mut tree);

// set duplication
tree.arena[a].e = Event::Duplication;
println!("");
println!("Event associated to gene {} ({}) : {:?}",a,tree.arena[a].name,tree.arena[a].e);
// Display internal nodes
options.gene_internal = true ;
phyloxml_processing(&mut tree, &options, &config,"build_tree.svg".to_string());
println!("Please open output file 'build_tree.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

See: http://www.phyloxml.org/

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

Licence

CECILL: https://choosealicense.com/licenses/cecill-2.1/