tibljТуберкулез и болезни легкихTuberculosis and Lung Diseases2075-12302542-1506Медицинские знания и технологииtiblj-851Research ArticleОБЗОРЫREVIEWSПрограммное обеспечение для обработки данных полногеномного секвенирования микроорганизмовSoftware for processing of data of whole-genome sequence analysis of microorganismsСпринджукМ. В.SprindzhukM. V.

220012, г. Минск, ул. Сурганова, д. 6

Minsk

msprindzhuk@mail.ruСергеевР. С.SergeevR. C.

Minsk

noemail@neicon.ruДемидчикЮ. Е.DemidchikYu. E.

Minsk

noemail@neicon.ruЗалуцкаяО. М.ZalutskayaO. M.

Minsk

noemail@neicon.ruСкрягинА. Е.SkryaginA. E.

Minsk

noemail@neicon.ruСкрягинаА. М.SkryaginaA. M.

Minsk

noemail@neicon.ruГНУ «Объединенный институт проблем информатики НАН Беларуси»БеларусьUnified Research Institute of Information Technology ProblemsBelarus2016010220169424754Copyright © Спринджук М.В., Сергеев Р.С., Демидчик Ю.Е., Залуцкая О.М., Скрягин А.Е., Скрягина А.М., 20162016Спринджук М.В., Сергеев Р.С., Демидчик Ю.Е., Залуцкая О.М., Скрягин А.Е., Скрягина А.М.Sprindzhuk M.V., Sergeev R.C., Demidchik Y.E., Zalutskaya O.M., Skryagin A.E., Skryagina A.M.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://www.tibl-journal.com/jour/article/view/851

Представлен краткий обзор cовременного программного обеспечения, разработанного для целей анализа данных полных ­геномов микроорганизмов.

The article presents the brief review of the current software developed for data analysis of microorganisms’ whole genomes.

полногеномное секвенированиебиоинформатикаcеквенирование следующего поколенияwhole-genome sequence analysissequence analysis of the next generationbioinformaticsReferencesAbdennadher N., Boesch R. Porting PHYLIP phylogenetic package on the desktop GRID platform XtremWeb-CH // Stud. Health Technol. Inform. - 2007. - Vol. 126. - P. 55-64.Abdennadher N., Boesch R. Porting PHYLIP phylogenetic package on the desktop GRID platform XtremWeb-CH. Stud. Health Technol. Inform., 2007, vol. 126, pp. 55-64.Aranguren M. E. et al. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows // J. Biomed. Semantics. - 2013. - Vol. 4, № 1. - P. 2.Aranguren M.E. et al. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. J. Biomed. Semantics, 2013, vol. 4, no. 1, pp. 2.Bakker H. C. et al. A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. enterica serovar Montevideo pulsed-field gel electrophoresis type // Appl. Environ Microbiol. - 2011. - Vol. 77, № 24. - P. 8648-8655.Bakker H.C. et al. A whole-genome single nucleotide polymorphism-based approach to trace and identify outbreaks linked to a common Salmonella enterica subsp. enterica serovar Montevideo pulsed-field gel electrophoresis type. Appl. Environ Microbiol., 2011, vol. 77, no. 24, pp. 8648-8655.Bao J. et al. Efficient implementation of MrBayes on multi-GPU // Mol. Biol. Evol. - 2013. - Vol. 30, № 6. - P. 1471-1479.Bao J. et al. Efficient implementation of MrBayes on multi-GPU. Mol. Biol. Evol., 2013, vol. 30, no. 6, pp. 1471-1479.Boutet E. et al. UniProtKB/Swiss-Prot // Methods Mol. Biol. - 2007. - Vol. 406. - P. 89-112.Boutet E. et al. UniProtKB/Swiss-Prot. Methods Mol. Biol., 2007, vol. 406, pp. 89-112.Braconi Quintaje S., Orchard S. The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes // Mol. Cell. Proteomics. - 2008. - Vol. 7, № 8. - P. 1409-1419.Braconi Quintaje S., Orchard S. The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes. Mol. Cell. Proteomics, 2008, vol. 7, no. 8, pp. 1409-1419.Burland T. G. Dnastar’s Lasergene sequence analysis software // Methods Mol. Biol. - 2000. - Vol. 132. - P. 71-91.Burland T.G. Dnastar’s Lasergene sequence analysis software. Methods Mol.Biol., 2000, vol. 132, pp. 71-91.Chang C. C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets // Gigascience. - 2015. - Vol. 4. - P. 7.Chang C.C. et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience, 2015, vol. 4, pp. 7.Clewley J. P. Geneman of lasergene // Methods Mol. Biol. - 1997. - Vol. 70. - P. 189-196.Clewley J.P. Geneman of lasergene. Methods Mol. Biol., 1997, vol. 70, pp. 189-196.Clewley J. P. Macintosh sequence analysis software. DNAStar’s LaserGene // Mol. Biotechnol. - 1995. - Vol. 3, № 3. - P. 221-224.Clewley J.P. Macintosh sequence analysis software. DNAStar’s LaserGene. Mol. Biotechnol., 1995, vol. 3, no. 3, pp. 221-224.Clewley J. P., Arnold C. MEGALIGN. The multiple alignment module of lasergene // Methods Mol. Biol. - 1997. - Vol. 70. - P. 119-129.Clewley J P., Arnold C. MEGALIGN. The multiple alignment module of lasergene. Methods Mol. Biol., 1997, vol. 70, pp. 119-129.Cock P. J. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics // Bioinformatics. - 2009. - Vol. 25, № 11. - P. 1422-1423.Cock P.J. et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 2009, vol. 25, no. 11, pp. 1422-1423.Coletta A. et al. InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor // Genome Biol. - 2012. - Vol. 13, № 11. - P. R104.Coletta A. et al. InSilico DB genomic datasets hub: an efficient starting point for analyzing genome-wide studies in GenePattern, Integrative Genomics Viewer, and R/Bioconductor. Genome Biol., 2012, vol. 13, no. 11, pp. R104.Crabtree J. et al. Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG // Bioinformatics. - 2014. - Vol. 30, № 21. - P. 3125-3127.Crabtree J. et al. Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG. Bioinformatics, 2014, vol. 30, no. 21, pp. 3125-3127.Di Tommaso P. et al. Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud // Bioinformatics. - 2010. - Vol. 26, № 15. - P. 1903-1904.Di Tommaso P. et al. Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud. Bioinformatics, 2010, vol. 26, no. 15, pp. 1903-1904.Di Tommaso P. et al. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension // Nucleic Acids Res. - 2011. - Vol. 39, № 1. - P. W13-W17.Di Tommaso P. et al. T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Reseach, 2011, vol. 39, no. 1, pp. W13-W17.Etherington G. J. et al. Bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby // Bioinformatics. - 2015. - № 1. - P. 1-12.Etherington G.J. et al. Bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby. Bioinformatics, 2015, no. 1, pp. 1-12.Famiglietti M. L. et al. Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation // Hum. Mutat. - 2014. - Vol. 35, № 8. - P. 927-935.Famiglietti M.L. et al. Genetic variations and diseases in UniProtKB/Swiss-Prot: the ins and outs of expert manual curation. Hum. Mutat., 2014, vol. 35, no. 8, pp. 927-935.Fan S. B. et al. Using pLink to analyze cross-linked peptides // Curr. Protoc. Bioinformatics. - 2015. - Vol. 49. - P. 1-8.Fan S.B. et al. Using pLink to Analyze Cross-Linked Peptides. Curr. Protoc. Bioinformatics, 2015, vol. 49, pp. 1-8.Fukami-Kobayashi K., Saito N. How to make good use of CLUSTALW // Tanpakushitsu Kakusan Koso. - 2002. - Vol. 47, № 9. - P. 1237-1239.Fukami-Kobayashi K., Saito N. How to make good use of CLUSTALW. TanpakushitsuGaudet P. et al. Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase // Database (Oxford). - 2009. - Vol. 2009. - P. bap016.Kakusan Koso, 2002, vol. 47, no. 9, pp. 1237-1239.Golosova O. et al. Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses // Peer. J. - 2014. - Vol. 2. - P. e644.Gaudet P. et al. Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase. Database (Oxford). 2009, vol. 2009, pp. bap016.Goto N. et al. BioRuby: bioinformatics software for the Ruby programming language // Bioinformatics. - 2010. - Vol. 26, № 20. - P. 2617-2619.Golosova O. et al. Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses. Peer. J., 2014, vol. 2, pp. e644.Guo C. et al. Ugene, a newly identified protein that is commonly overexpressed in cancer and binds uracil DNA glycosylase // Cancer Res. - 2008. - Vol. 68, № 15. - P. 6118-6126.Goto N. et al. BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics, 2010, vol. 26, no. 20, pp. 2617-2619.Harmsen D. et al. RIDOM: comprehensive and public sequence database for identification of Mycobacterium species // BMC Infect. Dis. - 2003. - Vol. 3. - P. 26.Guo C. et al. Ugene, a newly identified protein that is commonly overexpressed in cancer and binds uracil DNA glycosylase. Cancer Res., 2008, vol. 68, no. 15, pp. 6118-6126.Harmsen D. et al. RIDOM: Ribosomal differentiation of medical micro-organisms database // Nucleic Acids Res. - 2002. - Vol. 30, № 1. - P. 416-417.Harmsen D. et al. RIDOM: comprehensive and public sequence database for identification of Mycobacterium species. BMC Infect. Dis., 2003, vol. 3, pp. 26.Harris S. R. et al. Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks // Nat. Biotechnol. - 2013. - Vol. 31, № 7. - P. 592-594.Harmsen D. et al. RIDOM: Ribosomal differentiation of medical micro-organisms database. Nucleic Acids Reseach, 2002, vol. 30, no. 1, pp. 416-417.Holland R. C. et al. BioJava: an open-source framework for bioinformatics // Bioinformatics. - 2008. - Vol. 24, № 18. - P. 2096-2097.Harris S.R. et al. Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks. Nat. Biotechnol., 2013, vol. 31, no. 7, pp. 592-594.Huelsenbeck J. P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees // Bioinformatics. - 2001. - Vol. 17, № 8. - P. 754-755.Holland R.C. et al. BioJava: an open-source framework for bioinformatics. Bioinformatics, 2008, vol. 24, no. 18, pp. 2096-2097.Jayadeepa R. M. et al. Review and research analysis of computational target methods using BioRuby and in silico screening of herbal lead compounds against pancreatic cancer using R programming // Curr. Drug. Metab. - 2014. - Vol. 15, № 5. - P. 535-543.Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 2001, vol. 17, no. 8, pp. 754-755.Jungo F. et al. The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data // Toxicon. - 2012. - Vol. 60, № 4. - P. 551-557.Jayadeepa R.M. et al. Review and research analysis of computational target methods using BioRuby and in silico screening of herbal lead compounds against pancreatic cancer using R programming. Curr. Drug. Metab., 2014, vol. 15, no. 5, pp. 535-543.Kaisers W. et al. rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples // Bioinformatics. - 2015. - Vol. 31, № 10. - P. 1663-1664.Jungo F. et al. The UniProtKB/Swiss-Prot Tox-Prot program: A central hub of integrated venom protein data. Toxicon. 2012, vol. 60, no. 4, pp. 551-557.Katoh K. et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform // Nucleic Acids Res. - 2002. - Vol. 30, № 14. - P. 3059-3066.Kaisers W. et al. rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples. Bioinformatics, 2015, vol. 31, no. 10, pp. 1663-1664.Kim D., Salzberg S. L. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts // Genome Biol. - 2011. - Vol. 12, № 8. - P. R72.Katoh K. et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Reseach, 2002, vol. 30, no. 14, pp. 3059-3066.Kim K. U. et al. Comparison of functional gene annotation of Toxascaris leonina and Toxocara canis using CLC genomics workbench // Korean. J. Parasitol. - 2013. - Vol. 51, № 5. - P. 525-530.Kim D., Salzberg S.L. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol., 2011, vol. 12, no. 8, pp. R72.Kleindienst R. et al. Highly efficient refractive Gaussian-to-tophat beam shaper for compact terahertz imager // Appl. Opt. - 2010. - Vol. 49, № 10. - P. 1757-1763.Kim K.U. et al. Comparison of functional gene annotation of Toxascaris leonina and Toxocara canis using CLC genomics workbench. Korean. J. Parasitol., 2013, vol. 51, no. 5, pp. 525-530.Kohli D. K., Bachhawat A. K. CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics // Nucleic Acids Res. - 2003. - Vol. 31, № 13. - P. 3501-3502.Kleindienst R. et al. Highly efficient refractive Gaussian-to-tophat beam shaper for compact terahertz imager. Appl. Opt., 2010, vol. 49, no. 10, pp. 1757-1763.Li H. et al. The Sequence Alignment/Map format and SAMtools // Bioinformatics. - 2009. - Vol. 25, № 16. - P. 2078-2079.Kohli D.K., Bachhawat A.K. CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics. Nucleic Acids Res., 2003, vol. 31, no. 13, pp. 3501-3502.Li K. B. ClustalW-MPI: ClustalW analysis using distributed and parallel computing // Bioinformatics. - 2003. - Vol. 19, № 12. - P. 1585-1586.Li H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics, 2009, vol. 25, no. 16, pp. 2078-2079.Lim A., Zhang L. WebPHYLIP: a web interface to PHYLIP // Bioinformatics. - 1999. - Vol. 15, № 12. - P. 1068-1069.Li K.B. ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics, 2003, vol. 19, no. 12, pp. 1585-1586.Lima T. et al. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot // Nucleic. Acids Res. - 2009. - Vol. 37. - P. 471-478.Lim A., Zhang L. WebPHYLIP: a web interface to PHYLIP. Bioinformatics, 1999, vol. 15, no. 12, pp. 1068-1069.Ling C. et al. MrBayes tgMC(3): a tight GPU implementation of MrBayes // PLoS One. - 2013. - Vol. 8, № 4. - P. e60667.Lima T. et al. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic. Acids Res., 2009, vol. 37, pp. 471-478.Magis C. et al. T-Coffee: Tree-based consistency objective function for alignment evaluation // Methods Mol. Biol. - 2014. - Vol. 1079. - P. 117-129.Ling C. et al. MrBayes tgMC(3): a tight GPU implementation of MrBayes. PLoS One, 2013, vol. 8, no. 4, pp. e60667.McCormick R. F. et al. RIG: Recalibration and Interrelation of Genomic Sequence Data with the GATK // G3 (Bethesda). - 2015. - Vol. 5, № 4. - P. 655-665.Magis C. et al. T-Coffee: Tree-based consistency objective function for alignment evaluation. Methods Mol. Biol., 2014, vol. 1079, pp. 117-129.Mellmann A. et al. Evaluation of RIDOM, MicroSeq, and Genbank services in the molecular identification of Nocardia species // Int. J. Med. Microbiol. - 2003. - Vol. 293, № 5. - P. 359-370.McCormick R.F. et al. RIG: Recalibration and Interrelation of Genomic Sequence Data with the GATK. G3 (Bethesda). 2015, vol. 5, no. 4, pp. 655-665.Notredame C. Computing multiple sequence/structure alignments with the T-coffee package // Curr. Protoc. Bioinformatics. - 2010. - Vol. 3. - P. 1-25.Mellmann A. et al. Evaluation of RIDOM, MicroSeq, and Genbank services in the molecular identification of Nocardia species. Int. J. Med. Microbiol., 2003, vol. 293, no. 5, pp. 359-370.Notredame C. et al. T-Coffee: A novel method for fast and accurate multiple sequence alignment // J. Mol. Biol. - 2000. - Vol. 302, № 1. - P. 205-217.Notredame C. Computing multiple sequence/structure alignments with the T-coffee package. Curr. Protoc., Bioinformatics, 2010, vol. 3, pp. 1-25.Notredame C., Suhre K. Computing multiple sequence/structure alignments with the T-coffee package // Curr. Protoc. Bioinformatics. - 2004. - Vol. 3. - P. 3-8.Notredame C. et al. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 2000, vol. 302, no. 1, pp. 205-217.Octavia S. et al. Delineating community outbreaks of Salmonella enterica serovar Typhimurium by use of whole-genome sequencing: insights into genomic variability within an outbreak // J. Clin. Microbiol. - 2015. - Vol. 53, № 4. - P. 1063-1071.Notredame C., Suhre K. Computing multiple sequence/structure alignments with the T-coffee package. Curr. Protoc., Bioinformatics, 2004, vol. 3, pp. 3-8.Ogden T. H., Rosenberg M. S. Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP* // Syst. Biol. - 2007. - Vol. 56, № 2. - P. 182-193.Octavia S. et al. Delineating community outbreaks of Salmonella enterica serovar Typhimurium by use of whole-genome sequencing: insights into genomic variability within an outbreak. J. Clin. Microbiol., 2015, vol. 53, no. 4, pp. 1063-1071.Okonechnikov K. et al. Unipro UGENE: a unified bioinformatics toolkit // Bioinformatics. - 2012. - Vol. 28, № 8. - P. 1166-1167.Ogden T.H., Rosenberg M.S. Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via ClustalW + PAUP*. Syst. Biol., 2007, vol. 56, no. 2, pp. 182-193.Oliver T. et al. Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW // Bioinformatics. - 2005. - Vol. 21, № 16. - P. 3431-3432.Okonechnikov K. et al. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics, 2012, vol. 28, no. 8, pp. 1166-1167.Pantosti A. Whole-genome sequencing may be key to abating hospital-based methicillin-resistant Staphylociccus aureus outbreaks // J. Pediatr. - 2013. - Vol. 162, № 5. - P. 1079-1080.Oliver T. et al. Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. Bioinformatics, 2005, vol. 21, no. 16, pp. 3431-3432.Pollier J. et al. Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures // Methods Mol. Biol. - 2013. - Vol. 1011. - P. 305-315.Pantosti A. Whole-genome sequencing may be key to abating hospital-based methicillin-resistant Staphylociccus aureus outbreaks. J. Pediatr. 2013, vol. 162, no. 5, pp. 1079-80.Prlic A. et al. BioJava: an open-source framework for bioinformatics in 2012 // Bioinformatics. - 2012. - Vol. 28, № 20. - P. 2693-2695.Pollier J. et al. Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures. Methods Mol. Biol., 2013, vol. 1011, pp. 305-315.Purcell S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses // Am. J. Hum Genet. - 2007. - Vol. 81, № 3. - P. 559-575.Prlic A. et al. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics, 2012, vol. 28, no. 20, pp. 2693-2695.Ramirez-Gonzalez R. H. et al. Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments // Source Code Biol. Med. - 2012. - Vol. 7, № 1. - P. 6.Purcell S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum Genet., 2007, vol. 81, no. 3, pp. 559-575.Renteria M. E. et al. Using PLINK for Genome-Wide Association Studies (GWAS) and data analysis // Methods Mol. Biol. - 2013. - Vol. 1019. - P. 193-213.Ramirez-Gonzalez R.H. et al. Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments. Source Code Biol. Med., 2012, vol. 7, no. 1, pp. 6.Retief J. D. Phylogenetic analysis using PHYLIP // Methods Mol. Biol. - 2000. - Vol. 132. - P. 243-258.Renteria M.E. et al. Using PLINK for Genome-Wide Association Studies (GWAS) and data analysis. Methods Mol. Biol., 2013, vol. 1019, pp. 193-213.Rius J. et al. A user-friendly web portal for T-Coffee on supercomputers // BMC Bioinformatics. - 2011. - Vol. 12. - P. 150.Retief J D. Phylogenetic analysis using PHYLIP. Methods Mol. Biol., 2000, vol. 132, pp. 243-258.Robinson J. T. et al. Integrative genomics viewer // Nat. Biotechnol. - 2011. - Vol. 29, № 1. - P. 24-26.Rius J. et al. A user-friendly web portal for T-Coffee on supercomputers. BMC Bioinformatics, 2011, vol. 12, pp. 150.Ronquist F. et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space // Syst. Biol. - 2012. - Vol. 61, № 3. - P. 539-542.Robinson J.T. et al. Integrative genomics viewer. Nat. Biotechnol., 2011, vol. 29, no. 1, pp. 24-26.Ronquist F., Huelsenbeck J. P. MrBayes 3: Bayesian phylogenetic inference under mixed models // Bioinformatics. - 2003. - Vol. 19, № 12. - P. 1572-1574.Ronquist F. et  al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol., 2012, vol. 61, no. 3, pp. 539-542.Ropelewski A. J. et al. MPI-PHYLIP: parallelizing computationally intensive phylogenetic analysis routines for the analysis of large protein families // PLoS One. - 2010. - Vol. 5, № 11. - P. e13999.Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 2003, vol. 19, no. 12, pp. 1572-1574.Rothganger J. et al. Ridom TraceEdit: a DNA trace editor and viewer // Bioinformatics. - 2006. - Vol. 22, № 4. - P. 493-494.Ropelewski A.J. et al. MPI-PHYLIP: parallelizing computationally intensive phylogenetic analysis routines for the analysis of large protein families. PLoS One, 2010, vol. 5, no. 11, pp. e13999.Schneider M. et al. The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program // J. Proteomics. - 2009. - Vol. 72, № 3. - P. 567-573.Rothganger J. et al. Ridom TraceEdit: a DNA trace editor and viewer. Bioinformatics, 2006, vol. 22, no. 4, pp. 493-494.Shi H. et al. Using Fisher’s method with PLINK «LD clumped» output to compare SNP effects across Genome-wide Association Study (GWAS) datasets // Int. J. Mol. Epidemiol. Genet. - 2011. - Vol. 2, № 1. - P. 30-35.Schneider M. et al. The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. J. Proteomics, 2009, vol. 72, no. 3, pp. 567-573.Stajich J. E. An Introduction to BioPerl // Methods Mol. Biol. - 2007. - Vol. 406. - P. 535-548.Shi H. et al. Using Fisher’s method with PLINK «LD clumped» output to compare SNP effects across Genome-wide Association Study (GWAS) datasets. Int. J. Mol. Epidemiol., Genet. 2011, vol. 2, no. 1, pp. 30-35.Stajich J. E. et al. The Bioperl toolkit: Perl modules for the life sciences // Genome Res. - 2002. - Vol. 12, № 10. - P. 1611-1618.Stajich J.E. An Introduction to BioPerl. Methods Mol. Biol., 2007, vol. 406, pp. 535-548.Talevich E. et al. Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython // BMC Bioinformatics. - 2012. - Vol. 13. - P. 209.Stajich J.E. et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res., 2002, vol. 12, no. 10, pp. 1611-1618.Taly J. F. et al. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures // Nat. Protoc. - 2011. - Vol. 6, № 11. - P. 1669-1682.Talevich E. et al. Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics, 2012, vol. 13, pp. 209.Thompson J. D. et al. Multiple sequence alignment using ClustalW and ClustalX // Curr. Protoc. Bioinformatics. - 2002. - Vol. 2. - P. Unit 2 3.Taly J.F. et al. Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nat. Protoc., 2011, vol. 6, no. 11, pp. 1669-1682.Thorvaldsdottir H. et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration // Brief Bioinform. - 2013. - Vol. 14, № 2. - P. 178-192.Thompson J.D. et al. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinformatics, 2002, vol. 2, pp. Unit 2 3.Trapnell C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks // Nat. Protoc. - 2012. - Vol. 7, № 3. - P. 562-578.Thorvaldsdottir H. et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform., 2013, vol. 14, no. 2, pp. 178-192.Trapnell C. et al. TopHat: discovering splice junctions with RNA-Seq // Bioinformatics. - 2009. - Vol. 25, № 9. - P. 1105-1111.Trapnell C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with  TopHat and  Cufflinks. Nat. Protoc., 2012, vol. 7, no. 3, pp. 562-578.Vangala R. K. et al. BioParishodhana: A novel graphical interface integrating BLAST, ClustalW, primer3 and restriction digestion tools // Bioinformation. - 2012. - Vol. 8, № 13. - P. 639-643.Trapnell C. et al. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 2009, vol. 25, no. 9, pp. 1105-1111.Vaskin Y. Y. et al. ExpertDiscovery and UGENE integrated system for intelligent analysis of regulatory regions of genes // In Silico. Biol. - 2011. - Vol. 11, № 3-4. - P. 97-108.Vangala R.K. et al. BioParishodhana: A novel graphical interface integrating BLAST, ClustalW, primer3 and restriction digestion tools. Bioinformation, 2012, vol. 8, no. 13, pp. 639-643.Walker T. M. et al. Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing // Clin. Microbiol. Infect. - 2013. - Vol. 19, № 9. - P. 796-802.Vaskin Y.Y. et al. ExpertDiscovery and UGENE integrated system for intelligent analysis of regulatory regions of genes. In Silico. Biol., 2011, vol. 11, no. 3-4, pp. 97-108.Walker T. M. et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study // Lancet Infect. Dis. - 2013. - Vol. 13, № 2. - P. 137-146.Walker T.M. et al. Contact investigations for outbreaks of Mycobacterium tuberculosis: advances through whole genome sequencing. Clin. Microbiol. Infect., 2013, vol. 19, no. 9, pp. 796-802.Wallace I. M. et al. M-Coffee: combining multiple sequence alignment methods with T-Coffee // Nucleic. Acids Res. - 2006. - Vol. 34, № 6. - P. 1692-1699.Walker T.M. et al. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect. Dis., 2013, vol. 13, no. 2, pp. 137-146.Wang L. T. et al. Functional interaction of Ugene and EBV infection mediates tumorigenic effects // Oncogene. - 2011. - Vol. 30, № 26. - P. 2921-2932.Wallace I.M. et al. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic. Acids Res., 2006, vol. 34, no. 6, pp. 1692-1699.Wheelan S. J. et al. Spidey: a tool for mRNA-to-genomic alignments // Genome Res. - 2001. - Vol. 11, № 11. - P. 1952-1957.Wang L.T. et al. Functional interaction of Ugene and EBV infection mediates tumorigenic effects. Oncogene, 2011, vol. 30, no. 26, pp. 2921-2932.Zhou J. et al. MrBayes on a graphics processing unit // Bioinformatics. - 2011. - Vol. 27, № 9. - P. 1255-1261.Wheelan S.J. et al. Spidey: a tool for mRNA-to-genomic alignments. Genome Res., 2001, vol. 11, no. 11, pp. 1952-1957.Zhu P. et al. OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data // PLoS One. - 2014. - Vol. 9, № 5. - P. e97507.Zhou J. et al. MrBayes on a graphics processing unit. Bioinformatics, 2011, vol. 27, no. 9, pp. 1255-1261.Zhu P. et al. OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data. PLoS One, 2014, vol. 9, no. 5, pp. e97507.Zhu P. et al. OTG-snpcaller: an optimized pipeline based on TMAP and GATK for SNP calling from ion torrent data. PLoS One, 2014, vol. 9, no. 5, pp. e97507.

The authors declare that there are no conflicts of interest present.