PARLE: Path Analysis, Reconciliation, and Label Evaluation

This tool computes the path-label reconciliation (PLR) dissimilarity measure. (see abstract).

Reference: López Sánchez A., Ramírez-Rafael J. A., Flores Lamas A., Hernandez-Rosales M., Lafond M. (2024) The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees (currently under review at the WABI 2024 conference).

Installation

pip install parle

Synopsis of the tool

This code is a command-line tool designed to generate and compare reconciled gene trees with a given species tree, accounting for evolutionary events. It uses a proposed semi-metric PLR to quantify differences between reconciled gene trees, considering discrepancies in tree topology, gene-species mapping, and speciation/duplication events.

This tool supports benchmarking and validation by simulating reconciliations and comparing results with metrics like LRF and ELRF. The tool aims to enhance phylogenetic reconciliation by providing a refined and efficient method for comparing reconciled gene trees.

The tool can be used with the following syntax:

# Compute disimilarity
python -m parle gene_trees species_tree <optional arguments>

# Compute distance
python -m parle.simulate_reconciliations species_tree n_genes n_recons <optional arguments>

For detailed usage information, you can access the help documentation of the modules:

python -m parle -h
python -m parle.simulate -h

Tutorial

We will see how to generate and analyze datasets for 10 species, maximum 2 gene per species, and 20 gene trees/pairs of gene trees. These numbers can be modified.

The species tree can be simulated by PARLE or can be inputed as a .nhx file.

To Generate Data

Generate a list of reconciliations with the same species tree and set of genes for all the reconciliations:

python -m parle.simulate 10 2 20

Output files: plr.species_tree.list.nhx, plr.random_reconciliations.list.tsv

Generate pairs of reconciliations with the same species tree for all the reconciliations and pair-specific sets of genes:

python -m parle.simulate 10 2 20 -m pairs

Output files: plr.species_tree.pairs.nhx, plr.random_reconciliations.pairs.tsv.

To use an external species tree use the name of the file instead of 5, an example, if you have a file species_tree.nhx with the content ((((((16,17)15,14)7,6)5,((10,11)9,8)4)3,((18,19)13,12)2)1)0;, then you can use the commands:

python -m parle.simulate species_tree.nhx 1 10
python -m parle.simulate species_tree.nhx 1 10 -m pairs

To Compute Distances

Compute distances of pairs of trees sorted by rows:

python -m parle plr.random_reconciliations.list.tsv plr.species_tree.list.nhx

Compute distances for all possible pairs of gene trees in a list:

python -m parle plr.random_reconciliations.list.tsv plr.species_tree.list.nhx -m all_vs_all

Visualization

• For gene tree visualization we recomend itol.
• For trees reconciliation we recommend REvolutionH-tl.

Additional Information

• The tool uses the PLR metric, which is designed to compare reconciled gene trees by taking into account all three components of reconciliations (tree topology, gene-species map, and event labeling) as well as duplication clusters.

• The metric is linear-time computable, making it suitable for large datasets.

• For more detailed documentation and examples, please refer to the project documentation within the repository.