# rectree3


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OBSOLETE: Pease see 'thirdkind' instead! 
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https://github.com/simonpenel/thirdkind
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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.

https://raw.githubusercontent.com/simonpenel/rectree3/df6be6460cdacff21d06d72934828d0d1b422fe5/mapped_1.example.svg

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

https://raw.githubusercontent.com/simonpenel/rectree3/f609d9abc0819e0655b7b978dfc7eae2a23ea772/mapped_2.example.svg


# 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

See: http://www.phyloxml.org/

phyloXML paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774328/

# Under development:

- Multiple parasites



# Licence
CECILL: https://choosealicense.com/licenses/cecill-2.1/