reconcILS

Reconcile Gene Tree with Species Tree

Requirements

This package has the following requirements:

• Python (3.x)
• Pandas
• Matplotlib
• uuid
• igraph

Installation

You can install reconcILS using pip:

pip install .

Install the package via Conda:

conda install -c smishra677 reconcils

Arguments

Argument	Description	Required	Default Value
--spTree	Species tree in string // Location to Species Tree	Yes	N/A
--gTree	Gene tree in string // Location to Gene Tree	Yes	N/A
--output	Name of the output file with the extension .csv	Yes	N/A
--D	Duplication Cost	No	1.1
--L	Loss Cost	No	1.0
--I	ILS Cost	No	1.0
--V	Verbose Mode	No	0
--F	Input as file(--F 1 for file input)	No	0

Output

The tool generates a CSV output file with the following columns:

• Process
• Replicate (By Default :0)
• Labeled Gene_tree
• Species_Tree
• Number of Duplications
• Number of NNI (Nearest Neighbor Interchange)
• Number of Losses

Example entry in the output file:

output.csv

Process	Replicate	Gene_tree	Species_Tree	Duplication	NNI	Loss
reconcILS	0	"((C,A)1I C,B); "	"((0-0-0 C,0-0-0 B)0-1-0 ,0-0-0 A)0-0-0 ;"	0	1	0

output_log.csv

Gene_Tree	Species_Tree	Duplication_cost	NNI_cost	Loss_cost
"(B,(C,A));"	"(A,(B,C));"	1.1	1.0	1

Parsing Output

Labeled Species Tree

((0-0-0 C, 0-0-0 B) 0-1-0, 0-0-0 A) 0-0-0

Here, reconcILS produces a labeled species tree where each branch is labeled with the number of Duplication-NNI-Loss events for that branch. For instance, ((0-0-0 C, 0-0-0 B) 0-1-0, 0-0-0 A) 0-0-0 indicates there was one NNI move on the branch leading from (B, C) to (A, (B, C)) on the species tree.

Labeled Gene Tree

((C, A) 1I C, B)

Here, reconcILS labels the gene tree with Duplication (D), NNI (I), and Loss (L) events. For example, ((C, A) 1I C, B) indicates there was one NNI move on C at the branch (C, A) to (A, (B, C)) on the gene tree.

These labeled trees can be visualized with any Newick visualizer.

Experiments:

For experiments, please see the experiment branch. (https://github.com/smishra677/reconcILS/blob/Experiments/Experiments.md)

Example Usage

You can use reconcILS as follows:

Input as String:

python ./reconcILS/reconcILS.py --spTree '(A,(B,C));' --gTree '((A,C),B);' --output 'result.csv'

Input as file:

python ./reconcILS/reconcILS.py --spTree './spTree.tre' --gTree './gTree.tre' --output 'result.csv' --F 1

Using reconcILS from a Python file:

Please see the example.md at https://github.com/smishra677/reconcILS/blob/main/reconcILS/example/example.md

Example Usage Conda

Use the package programmatically from Python:

import sys
from reconcILS import reconcILS

# Simulate command-line arguments
sys.argv = [
    "reconcILS.py",
    "--spTree", "(A,(B,C));",     # Species tree in Newick format
    "--gTree", "((A,C),B);",      # Gene tree in Newick format
    "--output", "result.csv"      # Output file name
]

# Run the reconciliation
reconcILS.main()

This will generate:

• result.csv: Reconciliation summary including duplications, losses, and ILS events
• result_log.csv: Metadata log including input trees and cost parameters
• resultspecies_acr.json and resultacr_species.json: Mappings of species names to acronyms (if needed)

This interface allows calling reconcILS directly from Python scripts or notebooks (e.g., Google Colab), without using the command line.