ePLACE Documentation

ePLACE (environmental Phylogenetic Localisation and Clade Estimation) is a Python library for analyzing environmental DNA (eDNA) sequences through BLAST comparison and taxonomic classification.

Overview

ePLACE provides a comprehensive toolkit for environmental DNA analysis with the following capabilities:

NCBI Database Management: Download and manage NCBI BLAST databases (core_nt)
FASTA File Processing: Read and validate FASTA files
BLAST Search: Run blastn searches with configurable parameters
Result Filtering: Filter BLAST results by identity and coverage thresholds
Taxonomic Analysis: Extract representative sequences per taxonomic rank
Sequence Extraction: Retrieve sequences from BLAST databases
Sequence Trimming: Trim reference sequences to aligned regions based on BLAST coordinates
Multiple Sequence Alignment: Align sequences using MAFFT with auto-orientation
Phylogenetic Trees: Build and label phylogenetic trees using IQTree
Tree Relabeling: Relabel existing trees with taxonomic names at different ranks
Results Summary Output: Creates a tab separated output that summarises the per-sequence matches

Quick Start

Installation

Basic Usage

# Download NCBI database
eplace download

# Run search analysis (BLAST by default)
eplace search query.fasta output_dir

# Run grouped analysis
eplace grouped query.fasta output_dir --group-rank order

# Relabel existing tree with taxonomic names
eplace relabel blast_results.txt input.treefile output.treefile --rank genus

Table of Contents

API Reference

API Reference

Additional Information