Stéphane Samson1, Étienne Lord2, Vladimir Makarenkov1. 1. Department of Computer Sciences, Université du Québec à Montréal, Montreal, QC, Canada. 2. Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC, Canada.
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 Φ, Max-χ2, 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).
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 Φ, Max-χ2, 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).