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#8 in #phylogeny
290KB
342 lines
rectree2svg
OBSOLETE: Pease see 'thirdkind' instead! https://crates.io/crates/thirdkind
https://github.com/simonpenel/thirdkind
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 (rooted tree only) or phyloxml file: create a svg representation of the gene tree only .
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:
multiple gene trees with redundant transfers. Display only 1 gene tree and the transfers according to the abundance of the transfer:
Install:
rectree2svg is written in Rust. The code is managed using Cargo and published on crates.io.
Install cargo:
curl https://sh.rustup.rs -sSf | sh
or for Windows see https://doc.rust-lang.org/cargo/getting-started/installation.html
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][-F format][-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
-F phylo/recphylo: force format phyloXML/recPhyloXML
-g <n> : display the gene #n in phyloxml style (no species tree)
-h : help
-H height : multiply the tree height by factor 'height' (default 1.0)
-i : display internal gene nodes
-I : display internal species nodes
-J : with option -t, display the abundance of redudant transfers
-L : display as landscape
-l factor: use branch length, using the given factor
-o outputfile : set name of output file
-O switching nodes in order to minimise transfer crossings (under development)
-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
-S : display node support
-t <t> : redudant transfers are displayed as one, with opacity according to abundance and only if abundance is higher tan t. Only one gene is displayed.
-T <n> : with option -t, select the gene to display
-v : verbose
-W width : multiply the tree width by factor 'width' (default 1.0)
Input format is guessed according to the file name extension:
- .phyloxml => phyloXML
- .xml => recPhyloxml
- .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 API:
rectree2svg use the light_phylogeny crate:
https://crates.io/crates/light_phylogeny
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:
- Allow 2/3 reconciliation levels (host/species/gene)
Licence
Dependencies
~8–19MB
~238K SLoC