jcbontemps/phylogenetictree

Compute phylogenetic trees from distance matrix using BioNJ algorithm. It produce Newick file and Weighted newick if needed. There is also a render using Equal-angle algorithm and SVG output for testing. It's recommended to use a JS render like 'phylotree.js' (demo of phylotree.js here http://phylot

1.0.2 2024-11-25 02:00 UTC

Requires

• php: >=8.2
• ext-bcmath: *

Requires (Dev)

• php-parallel-lint/php-console-highlighter: ^1.0
• php-parallel-lint/php-parallel-lint: ^1.4
• phpstan/phpstan: ^2.0
• squizlabs/php_codesniffer: ^3.10
• yoast/phpunit-polyfills: ^3.0

GPL-3.0-or-later

README

Description

Compute phylogenetic trees from distance matrix using BioNJ algorithm.
It will produce Newick file and Weighted newick if needed.

There is also a render using Equal-angle algorithm and SVG output for testing.
It's preferred to use a JS render like 'phylotree.js' (demo of phylotree.js here http://phylotree.hyphy.org/).

Installation

composer require jcbontemps/phylogenetictree

How to use

We have this image representing locations:

We compute the pixel distance between each point:

	a	b	c	d	e	f
a	0	184	222	177	216	231
b	184	0	45	123	128	200
c	222	45	0	129	121	203
d	177	123	129	0	46	83
e	216	128	121	46	0	83
f	231	200	203	83	83	0

This file is saved in ./tests/distance_matrix_pixels.csv in CSV format with ; as separator.

We can use this code to print newicks:

$distance_matrix = BioNJ::distanceCsvToArray('./test/distance_matrix_pixels.csv');
$distance_matrix = BioNJ::normalizeMatrix($distance_matrix, 'auto');
$tree = BioNJ::BioNJ($distance_matrix);
$Newick = $tree->Newick;
echo "Newick generated:"."\n";
echo $Newick."\n";
$NewickW = $tree->newickWeight();
echo "Weighted newick generated:"."\n";
echo $NewickW."\n";

We can use the test render to print this SVG tree:

$render = new EqualAngle();
$svg = $render->compute($tree, 1024, 768, 100, 100, 24, []);
file_put_contents('./test/distance_matrix_pixels.svg', $svg);

It will produce this image:

The other produced image from US Cities:

You can see the complete example in ./tests/testBioNJ.php

License

Copyright (C) 2024  jcbontemps

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.