Embeds phylogenetic tree distances and produce representations
Project description
PEAR - Phylogeny Embedding and Approximate Representation ![]()
by Goldman group - EMBL-EBI
PEAR can:
- Compute the distance matrix given a set of phylogenetic trees;
- 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
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