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SimPlot specifications


Unique identifier OMICS_34169
Name SimPlot
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Version 3.5.1
Stability Stable
Registration required Yes
Maintained Yes




No version available


  • person_outline Stuart Ray

Publication for SimPlot

SimPlot citations


Novel canine circovirus strains from Thailand: Evidence for genetic recombination

Sci Rep
PMCID: 5951951
PMID: 29760429
DOI: 10.1038/s41598-018-25936-1
call_split See protocol

[…] value at 0.01. Bonferroni correction was used as a general setting. The complete genomes of CanineCV’s available in GenBank were included in the RDP analyses. Similarity plot and bootscan analysis in SIMPLOT software package version 3.5.1 were also performed on CanineCV sequences. Briefly, a bootscaning analysis was performed on four groups of complete CanineCV genome sequences based on differenti […]


High prevalence of HIV 1 transmitted drug resistance among therapy naïve Burmese entering travelers at Dehong ports in Yunnan, China

BMC Infect Dis
PMCID: 5941624
PMID: 29739342
DOI: 10.1186/s12879-018-3130-9

[…] n Program available from the HIV database ( The suspected novel recombinant strains were subjected to boot scanning and informative-site analysis using SimPlot version 3.5.1 with boot-scan window sizes of 200 bases, a step size of 20 bases and 100 replicates []. […]


A traditional evolutionary history of foot and mouth disease viruses in Southeast Asia challenged by analyses of non structural protein coding sequences

Sci Rep
PMCID: 5915611
PMID: 29691483
DOI: 10.1038/s41598-018-24870-6

[…] in NSP coding regions clustered with a different lineage monophyletic group, it was considered an inter-lineage ‘recent recombinant’, and analysis of specific recombination was further explored using Simplot with a 200–300 nt sliding window. Bayesian phylogenetic analyses were run using computational resources available in CIPRES. Genetic distances of nucleotide sequences were computed using the K […]


HIV 1 transmission networks across Cyprus (2010 2012)

PLoS One
PMCID: 5912776
PMID: 29684083
DOI: 10.1371/journal.pone.0195660
call_split See protocol

[…] de evolution with the “CAT” approximation for different evolutionary rates across sites []. To explore putative recombinant patterns in the viral sequences, we performed a bootscanning analysis using SimPlot (version3.5.1) []. Putative recombinants were confirmed by phylogenetic analysis using partial fragments showing discordant phylogenetic signals against a reference set of HIV-1 group pure sub […]


Frequency of occurrence of HIV 1 dual infection in a Belgian MSM population

PLoS One
PMCID: 5889168
PMID: 29624605
DOI: 10.1371/journal.pone.0195679

[…] ts 16 and 35 (). Highlighter plots () showed patterns highly suggestive for recombination between the initial and superinfecting strains in patients 16, 66 and 35, an assumption that was confirmed by Simplot analysis. The presence of recombinants explains the further branching of the tree. In patient 16, 50 and 66 all sequences were identified as subtype B. In patient 35 and 08 respectively the in […]


Molecular epidemiology and temporal evolution of norovirus associated with acute gastroenteritis in Amazonas state, Brazil

BMC Infect Dis
PMCID: 5879549
PMID: 29606095
DOI: 10.1186/s12879-018-3068-y
call_split See protocol

[…] in the MEGA 6 program []. The prototype sequences were obtained from GenBank database of the National Center for Biotechnology Information (NCBI). The recombination analyses were performed using the Simplot v. 3.5.1 program []. […]


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SimPlot institution(s)
National Institute of Virology, Pune, India; National AIDS Research Institute, Pune, India; Division of Infectious Diseases, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Center for Medical Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA; Viral and Rickettsial Diseases Laboratory, California Department of Health Services, Berkeley, CA, USA
SimPlot funding source(s)
Supported by the Fogarty International Center, National Institutes of Health (NIH), Program of International Training Grants in Epidemiology Related to AIDS, D43 TW0000, and by the HIVNET contract with Family Health International (FHI) with funds from the National Institute of Allergy and Infectious Diseases (NIAID), NIH grant N01-AI-35173-113 and NIAID grant 1 R01 AI41369-01A1.

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