This package is also available automatically when running code with npm run wppl or npm run sim.
It is a pure Node package (JavaScript) and can be used independently. phyjs provides a library of functions for working with phylogenetics in JavaScript.
The central function it provides is phyjs.read_phyjson(filename), a function for parsing a phylogenetic tree stored in the PhyJSON format, the novel format that we are using for storing phylogentic trees in this study.
The phyjs package also provides several phylogenetic trees as internal data structures (e.g. the Bisse_32 tree that is used for verification of the model scripts).
For the remaining functions of the package, read further.
TODO
NodeJS functions for phylogenetic trees.
Features: - reading in PhyJSON trees - working with phylogenetic trees - some useful mathematical functions
var my_tree = phyjs.read_phyjson("node_modules/phylodata/mesquite.phyjson")
phylodata.print_tree(my_tree)
var my_tree = phylodata.example_2
| Tree | Leaves | Age (Ma) | Description |
|---|---|---|---|
phyjs.bisse_32 |
32 | 13.0 | Example tree from Mesquite software |
phyjs.cetacean_87 |
87 | 35.9 | Cetacean tree from BAMMtools package |
phyjs.primates_233 |
233 | 65.1 | Primate tree from Diversitree package |
phyjs.example_2 |
2 | 2 | toy tree with two tips (no stalk) |
phyjs.primates_61 |
61 | Primate tree from Mesquite software (no stalk) |
To use the package it must be isntalled via npm install phyjs.
Use the phyjs. prefix to access the data and functions.