simphyni 0.1.0

SimPhyni: a tool for phylogenetic trait simulation and inference.

SimPhyNI

Overview

SimPhyNI (Simulation-based Phylogenetic iNteraction Inference) is a phylogenetically-aware framework for detecting evolutionary associations between binary traits (e.g., gene presence/absence, major/minor alleles, binary phenotypes) on microbial phylogenetic trees. This tool leverages phylogenetic infromation to correct for surious associations caused by the relatedness of sister taxa.

This pipeline is designed to:

• Infer evolutionary parameters for traits (gain/loss rates, time to emergence, ancestral states)
• Estimate trait co-occurence null models through independent simulation of traits
• Output statistical results for associations

---

Getting Started

Installation

Install using Conda:

conda install -c bioconda simphyni

Or using PyPI

pip install simphyni

Or install from source:

git clone https://github.com/jpeyemi/SimPhyNI.git
cd SimPhyNI
pip install .

test installation:

simphyni version

---

Directory Structure

SimPhyNI/
├── simphyni/               # Core package
│   ├── Simulation/          # Simulation scripts
│   ├── scripts/             # Workflow scripts
│   └── envs/simphyni.yaml   # Conda environment (used in snakemake)
├── conda-recipe/           # Build recipe 
├── snakemake_cluster_files # Cluster configs for Snakemake
└── pyproject.toml

---

Usage

Run mode (single-run)

simphyni run \
  --tree path/to/tree.nwk \
  --traits path/to/traits.csv \
  --runtype 0 \
  --outdir my_analysis \
  --cores 4 \
  --temp_dir ./temp \
  --min_prev 0.05 \
  --max_prev 0.95 \
  --prefilter \
  --plot

Run mode (batch)

Create a samples.csv file like:

Sample,Tree,Traits,RunType,MinPrev,MaxPrev
run1,tree1.nwk,traits1.csv,0,0.05,0.95
run2,tree2.nwk,traits2.csv,1,0.05,0.90

Then execute:

simphyni run --samples samples.csv --cores 8 --temp_dir ./temp

For all run options:

simphyni run --help

---

Outputs

Outputs are placed in structured folders in the working directory or specified output directory in the 3-Objects/ subdirectory, including:

• simphyni_result.csv contianing all tested trait pairs with their infered interaction direction, p-value, and effect size
• simphyni_object.pkl containinf the completed analysis, parsable with the attached environment (not recommended for large analyses, > 1,000,000 comparisons)
• heatmap summaries of tested associations if --plot is enabled

---

Contact

For questions, please open an issue or contact Ishaq Balogun at https://github.com/jpeyemi.