SimPlot++ (software)
SimPlot [1] is a Windows application allowing users to produce high-quality sequence similarity plots.
SimPlot++[2] is a freely available reinterpretation of SimPlot. SimPlot++ is an open-source multi-platform application developed at the department of Computer Science of the Université du Québec à Montréal. SimPlot++ 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.[3], χ2 [4], NSS [5] or proportion tests, and to generate and analyze interactive sequence similarity networks. SimPlot++ supports multicore data processing and provides useful distance calculability diagnostics. As such, SimPlot++ improves on the original tools offered by SimPlot, such as SimPlot, BootScan and FindSites, and provides users with a new similarity network feature[2]
SimPlot++ is available on github as source code from Windows, MacOS and Linux, and as an executable for Windows.
General Use
SimPlot++ requires a multiple sequence alignment input file containing either DNA or Amino acid sequences. The input data must be in one of the following formats: FASTA, Nexus, PIR, PHYLIP, Stockholm or Clustal.
Once loaded into SimPlot++, the input sequences must be manually separated into different groups by the user, based on their evolutionary proximity in order to generate consensus sequences.[6]. These consensus sequences will be used to perform any analysis available in SimPlot++. A minimum of two groups must be created in order to have full access to the application features[2]
References
- ↑ Lole, Kavita S.; Bollinger, Robert C.; Paranjape, Ramesh S.; Gadkari, Deepak; Kulkarni, Smita S.; Novak, Nicole G.; Ingersoll, Roxann; Sheppard, Haynes W.; Ray, Stuart C. (January 1999). "Full-Length Human Immunodeficiency Virus Type 1 Genomes from Subtype C-Infected Seroconverters in India, with Evidence of Intersubtype Recombination". Journal of Virology. 73 (1): 152–160. doi:10.1093/bioinformatics/btac287. ISSN 0022-538X. PMID 35451456 Check
|pmid=value (help). - ↑ 2.0 2.1 2.2 Samson, Stéphane; Lord, Étienne; Makarenkov, Vladimir (April 2022). "SimPlot++: a Python application for representing sequence similarity and detecting recombination". Bioinformatics. 38 (11): 3118–3120. arXiv:2112.09755. doi:10.1093/bioinformatics/btac287. PMID 35451456 Check
|pmid=value (help). - ↑ Bruen, Trevor C; Philippe, Hervé; Bryant, David (1 April 2006). "A Simple and Robust Statistical Test for Detecting the Presence of Recombination". Genetics. 172 (4): 2665–2681. doi:10.1534/genetics.105.048975. PMC 1456386. PMID 16489234.
- ↑ Smith, JohnMaynard (February 1992). "Analyzing the mosaic structure of genes". Journal of Molecular Evolution. 34 (2): 126–129. Bibcode:1992JMolE..34..126S. doi:10.1007/BF00182389. PMID 1556748. Unknown parameter
|s2cid=ignored (help) - ↑ Jakobsen, Ingrid B.; Easteal, Simon (1996). "A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences". Bioinformatics. 12 (4): 291–295. doi:10.1093/bioinformatics/12.4.291. PMID 8902355.
- ↑ Schneider, Thomas D. (2002). "Consensus Sequence Zen". Applied Bioinformatics. 1 (3): 111–119. ISSN 1175-5636. PMC 1852464. PMID 15130839.
External links
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