77 stable releases
| 3.5.0 | Feb 28, 2024 |
|---|---|
| 3.3.10 | Jan 23, 2024 |
| 3.3.9 | Dec 21, 2023 |
| 3.3.4 | Aug 28, 2023 |
| 1.8.0 | Jul 29, 2021 |
#101 in Parser implementations
320 downloads per month
3.5MB
1K
SLoC
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).
-
Input one newick or phyloxml file -> a svg representation of the tree with node events
-
Input one recphyloxml file -> a svg representation of the gene (or symbiot) 'lower' tree(s) inside the associated species (or host) 'upper' tree
-
Input a set of recphyloxml files -> a svg representation of all the gene (or symbiot) 'lower' tree(s) inside the associated species (or host) 'upper' tree, or only 1 gene tree with the transfers of all genes (or symbiotes) allowing to visualise transfers for different scenarios or histories.
-
Input two nested recphyloxml files -> several svg representations allowing to display 3 level reconciliations (for example gene/symbiot/host)
Homepage
homepage : https://github.com/simonpenel/thirdkind/wiki
Keywords:
phylogeny, reconciled trees, phylogenetic trees, reconciliation, visualisation, svg, recphyloxml, phyloxml, 3 levels reconciliation, gene transfer, speciation, duplication, loss
Formats:
phyloXML, recPhyloXML, rooted newick ( NHX balises will not be considered ).
Graphical interface
A web sever dedicated to the graphical interface of thirdkind is available here: http://thirdkind.univ-lyon1.fr/
Output examples of 2-levels visualisation:
single gene reconciliation with species tree:
the same gene reconciliation without the species tree:
multiple genes reconciliation:
real length with recPhyloXML file:
using a "free living" species:
multiple "spTree":
multiple gene trees reconciliation with redundant transfers. Display only 1 gene tree and the transfers in red with an opacity 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
Note:
Since Rust does not include its own linker yet,building thirdkind needs to have a C compiler like gcc installed to act as the linker. If it is note the case, install essential build needed by Rust:
sudo apt install build-essential
Once Cargo is installed just open a new terminal and type:
cargo install thirdkind
thirdkind
You may as well install from the sources. This may be useful if you want to use the examples. 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 [-a][-A stArt][-b][-B][-c config file][-d fontsize][-D fontsize][-e][-E][-F format][-g input file][-G #][-h][-H height][-i][-I][-J][-k symbol size][-K Bezier parameter][-l factor][-L][-m][-M][-N eNd][-o output file][-O][-p][-r ratio][-s][-S][-t threshold][-T #][-u threshold][-U #][-v][-W width]|-x][-X][-z thickness][-Z thickness]
-a : output the redundant transfers analysis
-A node name : display transfers starting from this node only
-b : open svg in browser
-B : with option -l, display branch length
-c configfile : use a configuration file
-d fontsize : set font size for gene trees
-D fontsize : set font size for species trees
-e : the node associated to FREE_LIVING are drawned in an external tree (free_living option) and superposed in case of multiple genes
-E : the node associated to FREE_LIVING are drawned in an external tree (free_living option) and shifted in case of multiple genes
-F phylo/recphylo : force format phyloXML/recPhyloXML
-g 2nd level input file (for example a gene-symbiote file with -f defining a symbiote-host file)
-G <n> : display the gene #n in phyloxml style (no species tree)
-h : help
-H height : multiply the tree height by factor 'height'
-i : display internal gene nodes
-I : display internal species nodes
-J : with option -t, display the abundance of redudant transfers
-k size: size of the circles, crosses, squares, etc.
-K Bezier parameter: curvature of the transfers and branches leading to free living organisms.
-l factor : use branch length, multiplied by the given factor
-L : display as landscape
-m : the input file (-f) is a list of recphyloxml files
-M : display duplication node at mid-distance in the branch (in progress)
-N node name : display transfers ending to this node only
-o outputfile/prefix : set the name of the output file/set the prefix of the output files
-O : switching nodes in order to minimise transfer crossings (under development)
-p : species 'upper' tree uniformisation
-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. If set to 0, no gene is displayed
-u <t> : with -g, same as -t, but apply to the '-f' input file, and -t will apply to the '-g' file
-U <n> : same as -T with -t, but for -u
-v : verbose
-W width : multiply the tree width by factor 'width'
-x : tidy mode (non-layered tidy tree layout)
-X : tidy mode, avoiding leave names superposition
-z thickness: thickness of the gene tree
-Z thickness: thickness of the species tree
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 files
For example you may input a gene-symbiote recphyloxml file with -g and symbiote-host recphyloxml file with -f
The -t/-u options are not totally implemented for the mapped_1/2/3 svg output files
Note on -x/-X options : the non-layered tidy tree layout is described in :
'van der Ploeg, A. 2014. Drawing non-layered tidy trees in linear time.
Software: Practice and Experience, 44(12): 1467–1484.'
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/hote_parasite_page4_BL.recphylo -b -l 1
thirdkind -f recphylo_examples/testfiles -m -b -t 3 -J
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
thirdkind -f newick_examples/virus.nhx -l 4 -b
thirdkind -f newick_examples/virus.nhx -l 4 -x -b
thirdkind -f newick_examples/virus.nhx -l 4 -X -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
Contents of a configuration file :
species_color:pink
species_opacity:0.9
single_gene_color:blue
gene_opacity:0.9
species_police_color:orange
species_police_size:12
gene_police_size:10
bezier:1
Using the API light_phylogeny:
thirdkind uses the light_phylogeny library:
https://github.com/simonpenel/light_phylogeny/wiki
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/
Citation
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac062/6525213
Contact
https://lbbe.univ-lyon1.fr/fr/annuaire-des-membres/penel-simon
Licence
Dependencies
~5–18MB
~215K SLoC