SimPlot++: a Python application for representing sequence similarity and detecting recombination

TL;DR

SimPlot++ is a versatile Python tool that visualizes sequence similarity, detects recombination events, and analyzes sequence networks, supporting multiple models and interactive features for evolutionary research.

Contribution

It introduces an open-source, multiplatform Python application with advanced features for sequence similarity visualization and recombination detection, enhancing existing tools.

Findings

Supports 63 nucleotide and 20 amino acid models

Detects recombination using Phi, Max-X2, NSS, and proportion tests

Provides interactive sequence similarity network analysis

Abstract

Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python, which can be used to produce publication quality sequence similarity plots using 63 nucleotide and 20 amino acid distance models, to detect intergenic and intragenic recombination events using Phi, Max-X2, NSS or proportion tests, and to generate and analyze interactive sequence similarity networks. SimPlot++ supports multicore data processing and provides useful distance calculability diagnostics. Availability: SimPlot++ is freely available on GitHub at: https://github.com/Stephane-S/Simplot_PlusPlus, as both an executable file (for Windows) and Python scripts (for Windows/Linux/MacOS).