#phylogeny #recphyloxml #tree-reconciliation #svg #bioinformatics

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

33 stable releases

new 2.3.3 Oct 13, 2021
2.3.2 Oct 12, 2021
2.2.4 Sep 30, 2021
2.2.2 Aug 12, 2021
1.0.7 Jun 24, 2021

#92 in Parser implementations

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CECILL-2.1

505KB
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thirdkind

Drawing reconciled phylogenetic trees allowing 1, 2 or 3 reconciliation levels

Homepage: https://github.com/simonpenel/thirdkind/wiki

thirdkind at crates.io

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 "path" gene (or symbiot) tree(s) inside the associated "pipe" species (or host) tree

  • Input two recphyloxml files -> several svg representations allowing to display 3 level reconciliations (for example gene/symbiot/host)

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 ).

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

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

Note:

Since Rust does not include its own linker yet, you need to have a C compiler like gcc installed to act as the linker.

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][-d fontsize][-D fontsize][-e][-F format][-g input file][-G #][-h][-H height][-i][-I][-J][-l factor][-L][-m][-o output file][-O][-p][-P][-r ratio][-s][-S][-t threshold][-T #][-u threshold][-U #][-v][-W width]

-b : open svg in browser
-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
-l factor : use branch length, multiplied by the given factor in case of newick/phyloxml,
            and by an optimised factor in case of recphyloxml
-L : display as landscape
-m : the input file (-f) is a list of recphyloxml files
-o outputfile : set name of output file
-O switching nodes in order to minimise transfer crossings (under development)
-p : build a phylogram
-P : pipe species 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.
-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'

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.

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

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/

Licence

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

Dependencies

~4–6.5MB
~122K SLoC