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

For output examples, please see home page https://github.com/simonpenel/thirdkind/wiki

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 [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, --merge <MERGE>
      	List of nodes to merge For example:
      	"PBIAU:PTETRD4,species_5:species_6"
-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
-P, --fill-species
      	Fill the species tree
-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" (Nodes should be
      	sorted from the top of the tree down to the leaves)
-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, --switch <SWITCH>
      	List of nodes whose left and right children will be switched For
      	example: "species_13", "species_14"
-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

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/free_living_reconciliated.recphylo -b  -e -L
thirdkind -f recphylo_examples/testfiles -m -b -t 3 -J
thirdkind -f paramecium_data/liste.txt -m -b -t 25 -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 recphylo_examples/recgs_dtl.recphyloxml  -b -n 3 -C
"#17387A,#8E3B8B,green" -k12 -q "5,6" -Q "black" -Z 1
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

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

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

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