:: DESCRIPTION
SOPanG (Shift-Or for Pan-Genome) is a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Cislak A, Grabowski S, Holub J.
SOPanG: online text searching over a pan-genome.
Bioinformatics. 2018 Dec 15;34(24):4290-4292. doi: 10.1093/bioinformatics/bty506. PMID: 29939210.
:: DESCRIPTION
PGAP (pan-genome analysis pipeline) can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters.
PGAP-X is a microbial comparative genomic analysis platform with graphic interface.
PGAweb is a webserver for bacterial pan-genome analysis. It had integrated our previous published stand-alone tools PGAP, PanGP and PGAP-X into one server and simplifies the analysis of pan-genome.
::DEVELOPER
Beijing Institute of Genomics, Chinese Acadamy of Sciences , Yongbing Zhao
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Chen X, Zhang Y, Zhang Z, Zhao Y, Sun C, Yang M, Wang J, Liu Q, Zhang B, Chen M, Yu J, Wu J, Jin Z, Xiao J.
PGAweb: A Web Server for Bacterial Pan-Genome Analysis.
Front Microbiol. 2018 Aug 21;9:1910. doi: 10.3389/fmicb.2018.01910. PMID: 30186253; PMCID: PMC6110895.
Zhao Y, Sun C, Zhao D, Zhang Y, You Y, Jia X, Yang J, Wang L, Wang J, Fu H, Kang Y, Chen F, Yu J, Wu J, Xiao J.
PGAP-X: extension on pan-genome analysis pipeline.
BMC Genomics. 2018 Jan 19;19(Suppl 1):36. doi: 10.1186/s12864-017-4337-7. PMID: 29363431; PMCID: PMC5780747.
Bioinformatics. 2012 Feb 1;28(3):416-8. doi: 10.1093/bioinformatics/btr655. Epub 2011 Nov 29.
PGAP: pan-genomes analysis pipeline.
Zhao Y1, Wu J, Yang J, Sun S, Xiao J, Yu J.
:: DESCRIPTION
PanGP is a tool for quickly analyzing bacterial pan-genome profile. It has integrated two kinds of sample algorithm, so that it could calculate the pan-genome profile of a population with dozens of or hundreds of strains at extremely low time-cost. At the same time, a user-friendly graphical interface was designed and the image about pan-genome profile could be drawn by PanGP directly.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 May 1;30(9):1297-9. doi: 10.1093/bioinformatics/btu017. Epub 2014 Jan 13.
PanGP: a tool for quickly analyzing bacterial pan-genome profile.
Zhao Y1, Jia X, Yang J, Ling Y, Zhang Z, Yu J, Wu J, Xiao J.
:: DESCRIPTION
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Roary: rapid large-scale prokaryote pan genome analysis.
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane JA, Parkhill J.
Bioinformatics. 2015 Nov 15;31(22):3691-3. doi: 10.1093/bioinformatics/btv421.
:: DESCRIPTION
Pan-Tetris is our interactive software tool that enables the visual inspection of gene occurrences in a pan-genome table. It allows the user to modify the composition of such pan gene groups with an aggregation technique that is inspired by the famous Tetris game.
::DEVELOPER
Research Group “Integrative Transcriptomics” , Center for Bioinformatics Tübingen, University of Tübingen
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2015;16 Suppl 11:S3. doi: 10.1186/1471-2105-16-S11-S3. Epub 2015 Aug 13.
Pan-Tetris: an interactive visualisation for Pan-genomes.
Hennig A, Bernhardt J, Nieselt K.
:: DESCRIPTION
EUPAN is a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2017 Aug 1;33(15):2408-2409. doi: 10.1093/bioinformatics/btx170.
EUPAN enables pan-genome studies of a large number of eukaryotic genomes.
Hu Z, Sun C, Lu KC, Chu X, Zhao Y, Lu J, Shi J, Wei C
:: DESCRIPTION
RPAN is a genome browser to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Nucleic Acids Res. 2017 Jan 25;45(2):597-605. doi: 10.1093/nar/gkw958. Epub 2016 Dec 10.
RPAN: rice pan-genome browser for ～3000 rice genomes.
Sun C et al.
