rectree2svg
Read, build, displays as svg and manipulates 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 the rectree2svg binary to draw trees to as well as the rust rectree2svg funtions to build, manipulate or draw phylogenetic trees (see "Using the code")
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:
Install:
rectree2svg is written in Rust. The code is managed using Cargo and published on crates.io. Once Cargo is installed just open a terminal and type:
cargo install rectree2svg
You may as well install from the sources. Clone or download the sources here https://github.com/simonpenel/rectree2svg and type:
cargo build --release
target/release/rectree2svg -h
Run the binary:
Read a newick, phyloxml or recPhyloXML file and create a svg.
Format is guessed according to filename (default is newick)
Usage:
rectree2svg -f input file [-b][-c config file][-g #][-h][-i][-I][-l factor][-o output file][-p][-r ratio][-s][-v]
-b : open svg in browser
-c configfile: use a configuration file
-g <n> : display the gene #n in phyloxml style (no species tree)
-h : help
-i : display internal gene nodes
-I : display internal species nodes
-l factor: use branch length, using the given factor
-o outputfile : set name of output file
-p : build a phylogram
-r ratio : set the ratio between width of species and gene tree.
Default 1.0, you usualy do not need to change it.
-s : drawing species tree only
-v : verbose
Input format is guessed according to the file name extension:
- .xml => phyloxml
- .phyloxml => phyloXML
- .recphyloxml => recPhyloXML
- .recPhyloXML => recPhyloXML
- .recphylo => recPhyloXML
- any other => newick
You will find several input file examples in newick_examples, recphylo_examples and xml_examples directories.
Configuration file:
You may configure some of the features of the svg with the -c option.
The default values are the values of the "config_default.txt" file.
Modify the default values and save it into "my_config.txt" then type:
rectree2svg -f recphylo_examples/FAM000600_reconciliated_big.recphylo -c my_config.txt -b
Using the code:
https://crates.io/crates/rectree2svg
You may find more code examples in the "examples" directory.
Simple Rust example: read a newick.txt file and creates the svg
use rectree2svg::{ArenaTree,Options,Config,newick2tree,knuth_layout,check_contour_postorder,
shift_mod_xy,set_middle_postorder,draw_tree};
use std::fs;
fn main() {
let mut tree: ArenaTree<String> = ArenaTree::default();
let options: Options = Options::new();
let config: Config = Config::new();
let contents = fs::read_to_string("newick.txt")
.expect("Something went wrong reading the newick file");
let root = tree.new_node("Root".to_string());
newick2tree(contents, &mut tree, root, &mut 0);
knuth_layout(&mut tree,root, &mut 1);
check_contour_postorder(&mut tree, root);
shift_mod_xy(&mut tree, root, &mut 0.0, &mut 0.0);
set_middle_postorder(&mut tree, root);
draw_tree(&mut tree,"my_svg.svg".to_string(),&options,&config);
}
Some newick examples are available here : https://github.com/simonpenel/rectree2svg/tree/master/newick_examples
Simple Rust example: build a gene tree with a duplication and creates the svg
use rectree2svg::{ArenaTree,Options,Config,Event,knuth_layout,check_contour_postorder,
cladogramme,shift_mod_xy,set_middle_postorder,draw_tree};
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 b = tree.new_node("b".to_string());
let c = tree.new_node("c".to_string());
let d = tree.new_node("d".to_string());
// 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();
// 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);
// set duplication
tree.arena[a].e = Event::Duplication;
knuth_layout(&mut tree,root, &mut 1);
// Display cladogram
cladogramme(&mut tree);
check_contour_postorder(&mut tree, root);
shift_mod_xy(&mut tree, root, &mut 0.0, &mut 0.0);
set_middle_postorder(&mut tree, root);
// Display internal nodes
options.gene_internal = true ;
draw_tree(&mut tree,"my_svg.svg".to_string(),&options,&config);
}
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/rectree2svg/
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)
- Allow 2/3 reconciliation levels (host/species/gene)
Tree drawing algorithms and structures
"Arena" Tree structure is inspired by the code proposed here
Tree drawing algorithms are well explained here and here