12 releases
0.5.3 | Feb 22, 2024 |
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0.5.2 | Feb 22, 2024 |
0.5.1 | Jun 24, 2021 |
0.4.0 | Jun 18, 2021 |
0.1.0 | Apr 20, 2021 |
#6 in #phylogeny
97 downloads per month
105KB
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rectree3
OBSOLETE: Pease see 'thirdkind' instead!
https://github.com/simonpenel/thirdkind
Build a svg representation of a 3 level reconciliation, as gene/parasite/host
Still in development
Keywords: phylogeny, reconciled trees, phylogenetic trees
Format and input files:
Input format is recPhyloXML
The program needs 2 input files: one for the gene/parasite reconciliation, one for the parasite/host reconciliation.
Output examples
The program creates 7 output files, including 2 files displaying the 3 levels all together:
mapped_1.svg display the recnociled genes trees inside the "pipe" parasite tree. The "pipe" trees shows the duplications, losses and transfers reletive to the host in a similar way the transfers are displayed in simple phyloXML format.
mapped_2.svg display the reconciled parasite trees inside the "pipe" host tree. The transfers between genes are mapped to the parasite tree and displayed
Install:
rectree3 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 rectree3
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/rectree3 -h
Run the binary:
Usage:
rectree3 -f parasite host input file -g gene parasite input file [-b][-c config file][-h][-i][-I][-L][-o output file][-r ratio][-v]
-b : open svg in browser
-c configfile: use a configuration file
-h : help
-i : display internal gene nodes
-I : display internal species nodes
-L : display as landscape
-r ratio : set the ratio between width of species and gene tree.
Default 1.0, you usualy do not need to change it.
-v : verbose
Example:
rectree3 -f recphyl_examples/test1_mult_parasite/rechp_dtl.recphyloxml -g recphyl_examples/test1_mult_parasite/recgs_mult_host_dtl.recphyloxml -i -b
You will find several input file examples in recphylo_examples directory.
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:
Using the API:
rectree3 use the light_phylogeny crate:
https://crates.io/crates/light_phylogeny
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:
- Multiple parasites
Licence
Dependencies
~8–18MB
~233K SLoC