# phyta-cli

> Console line interface that process phylogenetic trees metrics.

Latest version **1.0.6** (published 2017-09-24) · MIT license · 0 weekly downloads

## Install

```sh
npm install phyta-cli
pnpm add phyta-cli
yarn add phyta-cli
bun add phyta-cli
```

Provides the command `phyta-cli`.

## Health

**Score 15/100 (F)** — status: abandoned.

Positive: no vulnerabilities.

Warnings: low downloads; no types; no esm support.

Negative: abandoned; low maintenance score.

## Facts

| | |
|---|---|
| Version | 1.0.6 |
| Published | 2017-09-24 |
| First published | 2017-06-22 |
| Weekly downloads | 0 |
| License | MIT |
| TypeScript types | none |
| Module format | CommonJS |
| Dependencies | 3 |
| Known vulnerabilities | 0 (+1 in 1 direct dependencies) |
| Install scripts | no |
| GitHub stars | 0 |
| Author | Rafael Pereira, Ines Castro |
| Maintainers | inesgc, rafaelcpereira |
| Keywords | phylogenetic trees, metrics, robinson foulds, cli, phylo, newick, phylogeny, phylogenetic, triplet metric, quartet metric, compararison metrics |

## Links

- npm: https://www.npmjs.com/package/phyta-cli
- Repository: https://github.com/RafaelPereira94/phyta-cli
- Homepage: https://github.com/RafaelPereira94/phyta-cli#readme
- Issues: https://github.com/RafaelPereira94/phyta-cli/issues
- npm.io page: https://npm.io/package/phyta-cli

## Dependencies (3)

- [fs](https://npm.io/package/fs.md) 0.0.1-security
- [commander](https://npm.io/package/commander.md) latest
- [require-dir](https://npm.io/package/require-dir.md) ^0.3.2

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## Recent versions

- 1.0.6 (latest) — 2017-09-24
- 1.0.5 — 2017-06-28
- 1.0.4 — 2017-06-23
- 1.0.3 — 2017-06-23
- 1.0.2 — 2017-06-22
- 1.0.1 — 2017-06-22
- 1.0.0 — 2017-06-22

## README

# phyta-cli

[![NPM](https://nodei.co/npm/phyta-cli.png?downloads=true&downloadRank=true&stars=true)](https://nodei.co/npm/phyta-cli/)

Command line interface, that allows the user to process
trees with the metrics and parsers available.

**Install:**

In order to use the phyta-cli you need to install it globally in your machine using: 
>npm install -g phyta-cli

**Options:**
* **`-h, --help `**
Shows the usage information.

* **`-V, --version`**
Shows the CLI version number.

* **`-l, --path <path>`** 
Path to folder with files to be processed.

* **`-f, --trees <path>`** 
Path to file with trees to be processed.

* **`-t, --types <path>`**
Path to file with tree types.

* **`-m, --metrics <path>`**
Path to file with metrics.

* **`-p,  --parser <parser>`**
Parser to be used on the trees.

* **`-o,  --output <path>`**
Output path where the results will be saved.

All command options are required, if any one of them is missing an exception will be thrown.

**Usage example:**

In order to run PhytA-cli from command line, you must specify,the metrics that will be used, the trees and their types. Each one in a different file. 
All the metrics, trees and tree types are separated by `$` character.

**Tree file:**

>trees.txt 

>(A,B,(C,D)E)F;$(A,B,(C,D)E)F;

**Tree types file:**

>types.txt

>rooted$rooted

**Metrics file:**

>metrics.txt

>robinsonFoulds$robinsonFouldsLength

Using the files specified above, we can run CLI using this command:

> phyta-cli --path /Users/rafae/Desktop/Trees/ --trees trees.txt --types types.txt --metrics metrics.txt --parser newick --output results

**Results:**

Now we give more details about the trees inserted
 and we mark the similarities and dissimilarities between phylogenetic trees given by
 the json field diffsT1 and diffsT2.
 
**Supported metrics and parsers:**

Now we support four metrics!! Each are: Robinson–Foulds, Robinson–Foulds Length, triplet and quartet metric.

More parsers may be added in the future but for now only newick parser is supported.

**Web-application:**

If you desire to see the tree visualization and not only the result values,
we have [web application](http://cloud131.ncg.ingrid.pt:3000/home) temporally hosted.
Feel free to test it out and if possible give us some opinions and critics.

---
_Source: https://npm.io/package/phyta-cli · Machine-readable twin of the npm.io package page. Health data is recomputed on every publish._