rectree2svg
Build a svg representation of a phylogenetic reconciled (or not) tree
Keywords: phylogeny, reconciled trees, phylogenetic trees
Read a recphyloxml file: create a svg representation of the gene trees and species tree with events (loss, duplication, speciation, transfer).
Read a newick or phyloxml file: create a svg representation of the tree.
You may use the rectree2svg binary as well as the rust rectree2svg funtions (see "Using the code")
Currently under development.
Output example
Under development:
- Possible problem with obsolete recPhyloXML format (speciationLoss is supported , speciationOutLoss and speciationOut are not supported yet)
- Allow 2/3 reconciliation levels (host/species/gene)
Instructions:
- cargo build --release
- target/release/rectree2svg -h
Help:
Read a newick, phyloxml or recPhyloXML file and create a svg.
Format is guessed according to filename (default is newick)
Usage:
target/release/rectree2svg -f input file [-b][-h][-i][-I][-l factor][-o output file][-p][-s][-v]
-b : open svg in browser
-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
-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
Using the code
https://crates.io/crates/rectree2svg
Simple Rust example: read a newick.txt file and create the svg
use rectree2svg::{ArenaTree,Options,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 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);
}
Some newick examples are available here : https://github.com/simonpenel/rectree2svg/tree/master/newick_examples
Source documentation
See Rust documentation : https://docs.rs/rectree2svg/
RecPhyloXML documentation
See http://phylariane.univ-lyon1.fr/recphyloxml/
Tree drawing algorithms and structures
"Arena" Tree structure is inspired by the code proposed here