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#37 in Biology

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CECILL-2.1

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light_phylogeny at crates.io light_phylogeny at docs.rs light_phylogeny at docs.rs light_phylogeny at docs.rs License: GPL v2

light_phylogeny is a rust library dedicated to phylogeny.

You may :

  • Read, build, modify and displays as svg reconciled phylogenetic trees.

  • Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconciliation levels

  • 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 2 nested recphyloxml files: create svg representations of the gene tree(s), the associated symbiot 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.

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

Homepage

Formats:

phyloXML, recPhyloXML, rooted newick (NHX tags will not be considered).

Output examples

single gene reconciliation with species tree:

https://raw.githubusercontent.com/simonpenel/thirdkind/74b9c84a5b2ed84ff5230fc3a52af856b9aba53d/output_examples/thirdkind_example1.svg

the same gene reconciliation without the species tree:

https://raw.githubusercontent.com/simonpenel/thirdkind/74b9c84a5b2ed84ff5230fc3a52af856b9aba53d/output_examples/thirdkind_example1_bis.svg

multiple genes reconciliation:

https://raw.githubusercontent.com/simonpenel/thirdkind/70a7a11aa89eda61926c5cabf221f47bb44e3409/output_examples/thirdkind_example4.svg

example with "free living" species:

https://raw.githubusercontent.com/simonpenel/thirdkind/9eb47ce644998164ff56cc68eb765c0c8a24d389/output_examples/thirdkind_fl_example.svg

multiple gene trees reconciliation with redundant transfers. Display only 1 gene tree and the transfers in red with an opacity according to the abundance of the transfer:

https://raw.githubusercontent.com/simonpenel/thirdkind/70a7a11aa89eda61926c5cabf221f47bb44e3409/output_examples/thirdkind_example2.svg

For more examples, see the "thirdkind" software https://github.com/simonpenel/thirdkind.

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

Read and display a reconciled tree from a recPhyloXML file:

https://github.com/simonpenel/light_phylogeny/blob/master/examples/read_recphyloxml.rs

Source documentation

See Rust documentation : https://docs.rs/light_phylogeny/

The "thirdkind" software

https://github.com/simonpenel/thirdkind

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/

Dependencies

~3.5MB
~67K SLoC