pear-ebi 0.1.1.10

Embeds phylogenetic tree distances and produce representations

PEAR - Phylogeny Embedding and Approximate Representation

by Goldman group - EMBL-EBI

PEAR can:

1. Compute the distance matrix given a set of phylogenetic trees;
2. Embed and represent the distance matrix in 2D or 3D.

PEAR usage

PEAR as a program

Please, run python3 PEAR.py --help to see the complete list of arguments and flags.

Simple usage

python3 ./main.py examples_trees_sets/beast_trees_500_tips.txt --hashrf --pca 3 this script calculates the distances between the trees in the file "beast_trees_500_tips.txt", which contains 2001 phylogenetic trees. The flag "--hashrf" defines the use of HasRF algorithm to perform this task See HashRF documentation. The flag "--pca 3" indicates to the program to perform a Principal Coordinate Analysis to embed the distance matrix in 3 dimensions, returning the final coordinates in the lower-dimensional space and plotting them in 2D and 3D.

Interactive mode

python3 ./main.py examples_trees_sets/beast_trees_500_tips.txt --i this script launches the program in interactive mode. Once the program starts, it is going to guide you through its usage thanks to an intuitive interface.

PEAR as a python library