#phylogenetic #svg #bioinformatics #newick #tree-node #recphyloxml #phylogeny

app thirdkind

Read phylogenetic tree(s) in newick, phyloXML or recPhyloXML file and build a svg representation of the tree(s) allowing 1, 2 or 3 reconciliation levels

89 stable releases

3.6.8 May 30, 2024
3.5.0 Feb 28, 2024
3.3.9 Dec 21, 2023
3.3.4 Aug 28, 2023
1.8.0 Jul 29, 2021

#3 in Biology

Download history 198/week @ 2024-02-24 22/week @ 2024-03-02 11/week @ 2024-03-09 11/week @ 2024-03-16 4/week @ 2024-03-23 11/week @ 2024-03-30 291/week @ 2024-04-06 7/week @ 2024-04-13 239/week @ 2024-05-11 414/week @ 2024-05-18 845/week @ 2024-05-25 128/week @ 2024-06-01 8/week @ 2024-06-08

1,431 downloads per month

CECILL-2.1

4MB
1.5K 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

thirdkind at crates.io License: GPL v2

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:

https://raw.githubusercontent.com/simonpenel/thirdkind/74b9c84a5b2ed84ff5230fc3a52af856b9aba53d/output_examples/thirdkind_example1.svg

the same gene reconciliation without the species tree:

https://raw.githubusercontent.com/simonpenel/thirdkind/74b9c84a5b2ed84ff5230fc3a52af856b9aba53d/output_examples/thirdkind_example1_bis.svg

multiple genes reconciliation:

https://raw.githubusercontent.com/simonpenel/thirdkind/70a7a11aa89eda61926c5cabf221f47bb44e3409/output_examples/thirdkind_example4.svg

real length with recPhyloXML file:

https://raw.githubusercontent.com/simonpenel/thirdkind/b084872f02a758702e0f90543c715862729166a5/output_examples/thirdkind_real_length.svg

using a "free living" species:

https://raw.githubusercontent.com/simonpenel/thirdkind/0f8ff64838fc7676b2e98542e953c4ccc9f45c62/output_examples/thirdkind_fl_example2.svg

multiple "spTree":

https://raw.githubusercontent.com/simonpenel/thirdkind/79344589aa8b91a909386d22c95a01bc8c795396/output_examples/thirdkind_multspec.svg

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:

https://raw.githubusercontent.com/simonpenel/thirdkind/70a7a11aa89eda61926c5cabf221f47bb44e3409/output_examples/thirdkind_example2.svg

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 [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): 14671484.'

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/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

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/

Dependencies

~7–19MB
~271K SLoC