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 temporally hosted. Feel free to test it out and if possible give us some opinions and critics.