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 gene (or symbiot) 'lower' tree(s) inside the associated species (or host) 'upper' tree
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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.
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Input two nested recphyloxml files -> several svg representations allowing to display 3 level reconciliations (for example gene/symbiot/host)
homepage : https://github.com/simonpenel/thirdkind/wiki
phylogeny, reconciled trees, phylogenetic trees, reconciliation, visualisation, svg, recphyloxml, phyloxml, 3 levels reconciliation, gene transfer, speciation, duplication, loss
phyloXML, recPhyloXML, rooted newick ( NHX balises will not be considered ).
A web sever dedicated to the graphical interface of thirdkind is available here: http://thirdkind.univ-lyon1.fr/
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:
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
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
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
Read a newick, phyloxml or recPhyloXML file and create a svg.
Format is guessed according to filename (default is newick)
Usage: thirdkind [OPTIONS] --input-file <INPUT_FILE>
Options:
-a, --output-transfer-analysis
Display transfers analysis (with -m and -t options)
-A, --starting-node <STARTING_NODE>
Display transfers starting from this node only
-b, --browser
Open svg in browser
-B, --display-br-length
With option -l, display branch length
-c, --conf-file <CONF_FILE>
Use configuration file
-C, --gene-colors <GENE_COLORS>
Define colors for gene trees. For example: "red,violet,#4A38C4,orange"
-d, --gene-fontsize <GENE_FONTSIZE>
Set font size for gene trees
-D, --species-fontsize <SPECIES_FONTSIZE>
Set font size for species trees
-e, --free-living-sup
"free living" option : nodes associated to FREE_LIVING are drawned in an external tree and superposed in case of multiple genes
-E, --free-living-shi
"free living" option : nodes associated to FREE_LIVING are drawned in an external tree and shifted in case of multiple genes
-f, --input-file <INPUT_FILE>
Input tree file (accepted format: newick, phyloXML, recPhyloXML)
-F, --format <FORMAT>
Force format phyloXML/recPhyloXML
-g, --nested <NESTED>
1st level input file (for example a gene-symbiote file with -f defining a 2nd level symbiote-host file)
-G, --gene-phylo <GENE_PHYLO>
Display the gene number <GENE_PHYLO> in phyloxml style (no species tree)
-H, --height <HEIGHT>
Height: multiply the tree height by factor <HEIGHT>
-i, --internal-gene-node
Display internal gene node names
-I, --internal-species-node
Display internal species node names
-J, --display-transfers-abundance
With option -t, display the abundance of redudant transfers
-k, --symbol-size <SYMBOL_SIZE>
Size of the circles, crosses, squares, etc
-K, --bezier <BEZIER>
Bezier parameter: curvature of the transfers and branches leading to free living organisms
-l, --branch-length <BRANCH_LENGTH>
Use branch length, multiplied by the given factor
-L, --landscape
Display as landscape
-m, --multiple
The input file (-f) is a list of recphyloxml files
-M, --midway
Display duplication node at midway in the branch
-n, --gene-tree-list <GENE_TREE_LIST>
List of the indexes of the gene trees to be displayed. For example: 1,2,6,9. If 0, only the species ('upper') tree is displayed
-N, --ending-node <ENDING_NODE>
Display transfers ending to this node only
-o, --output <OUTPUT>
Set the name of the output file or the prefix of the output files
-O, --optimise
Switching nodes in order to minimise transfer crossings (under development)
-p, --uniform
Species tree uniformisation. All the branches of species have the same width
-q, --node-colors <NODE_COLORS>
Nodes to be coloured : the descendants of each nodes will be drawn with a different colour. For example: "m3,m25,m36"
-Q, --background <BACKGROUND>
Background colour
-r, --ratio <RATIO>
Set the ratio between width of species and gene tree. Default is 1.0, you usualy do not need to change it
-s, --species-only
Display species tree only in phyloxml style
-S, --node-support
Display node support
-t, --threshold <THRESHOLD>
Redudant transfers are displayed as one, with opacity according to abundance and only if abundance is higher than <THRESHOLD>. Only one gene is displayed
-T, --threshold-select <THRESHOLD_SELECT>
With option -t, select the index of the gene to display. If set to 0, no gene is displayed
-u, --threshold-nested <THRESHOLD_NESTED>
With -g, same as -t, but apply to the '-f' input file, and -t will apply to the '-g' file
-U, --threshold-nested-select <THRESHOLD_NESTED_SELECT>
Same as -T with -t, but for -u
-v, --verbose
Verbose mode
-W, --width <WIDTH>
Width: multiply the tree height by factor <WIDTH>
-x, --tidy
Tidy mode (non-layered tidy tree layout)
-X, --tidy-clean
Tidy mode, avoiding leave names superposition
-z, --gene-thickness <GENE_THICKNESS>
Thickness of the gene tree
-Z, --species-thickness <SPECIES_THICKNESS>
Thickness of the species tree
-h, --help
Print help
-V, --version
Print version
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 3-levels reconciliation 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
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
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
thirdkind uses the light_phylogeny library:
https://github.com/simonpenel/light_phylogeny/wiki
See http://phylariane.univ-lyon1.fr/recphyloxml/
recPhyloXML paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198865/
phyloXML paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774328/
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac062/6525213
https://lbbe.univ-lyon1.fr/fr/annuaire-des-membres/penel-simon
