thirdkind
Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconciliation levels
Build svg representations of phylogenetic reconciled (or not) trees with events (loss, duplication, speciation, transfer).
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Input one newick or phyloxml file -> a svg representation of the tree with node events
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Input one recphyloxml file -> a svg representation of the "path" gene (or symbiot) tree(s) inside the associated "pipe" species (or host) tree
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Input two recphyloxml files -> several svg representations allowing to display 3 level reconciliations (for example gene/symbiot/host)
Keywords: phylogeny, reconciled trees, phylogenetic trees
Formats:
phyloXML, recPhyloXML, rooted newick ( NHX balises will not be considered ).
Output examples of 2-levels visualisation:
single gene reconciliation in recphyloxml:
the same gene reconciliation in phyloxml:
multiple genes reconciliation recphyloxml:
multiple gene trees with redundant transfers. Display only 1 gene tree and the transfers according to the abundance of the transfer:
Output examples of 3-levels visualisation::
Example 1
reconciled symbiote tree with associated gene trees: https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example3_mapped_1.svg
symbiote-host reconciliation plus mapped gene transfers: https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example3_mapped_2.svg
host tree with associated gene trees: https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example3_mapped_3.svg
Example 2
reconciled symbiote trees with associated gene trees: https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example4_mapped_1.svg
symbiote-host reconciliation plus mapped gene transfers: https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example4_mapped_2.svg
host tree with associated gene trees: https://raw.githubusercontent.com/simonpenel/thirdkind/abfb9e6a28d03860bea43b52312dc706554fd53d/output_examples/thirdkind_example4_mapped_3.svg
Install:
thirdkind 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 thirdkind
You may as well install from the sources. Clone or download the sources here https://github.com/simonpenel/thirdkind and type:
cargo build --release
target/release/thirdkind -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:
thirdkind -f input file [-b][-c config file][-F format][-g input 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
-F phylo/recphylo: force format phyloXML/recPhyloXML
-g 2nd level input file
-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)
Note on -b option : you must set a browser as default application for opening svg file
Note on -g option : this will generate 3-levels reconciliation svg. For example you may input a gene-symbiote recphyloxml file with -g and symbiote-host recphyloxml file with -f
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 recphylo_examples and xml_examples directories.
Examples:
thirdkind -f recphylo_examples/FAM000297_reconciliated.recphylo -b
thirdkind -f recphylo_examples/concat.xml -b -t 0
thirdkind -f recphylo_examples/test2/hote_parasite_page2.recphylo -g recphylo_examples/test2/gene_parasite_page2.recphylo -b
thirdkind -f recphylo_examples/test1_mult_parasite/rechp_dtl.recphyloxml -g recphylo_examples/test1_mult_parasite/recgs_mult_host_dtl.recphyloxml -b
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:
thirdkind -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
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/