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PyamilySeq - A a tool to look for sequence-based gene families identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.

Project description

PyamilySeq

PyamilySeq (Family Seek) is a Python tool for clustering gene sequences into families based on sequence similarity identified by tools such as CD-HIT, DIAMOND or MMseqs2. This work is an extension of the gene family / pangenome tool developed for the StORF-Reporter publication in NAR (https://doi.org/10.1093/nar/gkad814).

Features

  • Clustering: Supports input from CD-HIT formatted files as well as TSV and CSV Edge List formats.
  • Reclustering: Allows for the addition of new sequences post-initial clustering.
  • Output: Generates a gene 'Roary' presence-absence CSV formatted file for downstream analysis.

Installation

PyamilySeq requires Python 3.6 or higher. Install dependencies using pip:

pip install PyamilySeq

Usage

Clustering Analysis

To perform clustering analysis:

python pyamilyseq.py -c clusters_file -f format

Replace clusters_file with the path to your clustering output file and format with one of: CD-HIT, CSV, or TSV.

Reclustering

To add new sequences and recluster:

PyamilySeq -c clusters_file -f format --reclustered reclustered_file

Replace reclustered_file with the path to the file containing additional sequences.

Output

PyamilySeq generates various outputs, including:

  • Gene Presence-Absence File: This CSV file details the presence and absence of genes across genomes.

Gene Family Groups

After analysis, PyamilySeq categorizes gene families into several groups:

  • First Core: Gene families present in all analysed genomes initially.
  • Extended Core: Gene families extended with additional sequences.
  • Combined Core: Gene families combined with both initial and additional sequences.
  • Second Core: Gene families identified only in the additional sequences.
  • Only Second Core: Gene families exclusively found in the additional sequences.

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