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Tools provided with UGENE installation
- BLAST , Smith - Waterman - popular basic local sequence alignment toolsa popular tool for searching similarities between biological sequences.
- HMMER2/HMMER3 - sequence analysis using profile hidden Markov Models models, constructed from multiple sequence alignments.
- ClustalW, ClustalO, MuscleMUSCLE, K-AlignKalign, MafftMAFFT, T-Coffee multiple sequence alignment algorithms.
- Repeat finding and sequence comparison algorithms with a convenient dot-plot based results visualization.
- Open reading frames visualization and export.
- Restriction sites visualization tool with included version of the integrated REBASE database.
- Transcription factor binding sites analysis with SITECON, weight-matrix based algorithms and included version of JASPAR database.
- Short read aligners: BWA, BWA-MEM, Bowtie, Bowtie2, UGENE AlignerTopHat, etc.
- GC-content, AT-content graphs.
- Mr bayes and Phylip MrBayes, Phylip and PhyML tools for phylogenetic trees construction.
- ... and dozens of other popular and highly cited tools.
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- The system requirements for UGENE are these:
- Operating system (32 or 64 bit): Windows, Mac OS, Linux.
- RAM:
- 512 Mb RAM is required.
- At least 2Gb RAM is recommended.
- Disk space:
Minimum The minimum required disk space depends on the UGENE package:- Standard package: 200-300 Mb
- Full package: 500-900 Mb
- NGS package: 21-24 Gb
In most cases it is recommended to use UGENE full package, as it embeds additional external tools, such as local BLAST, Bowtie, etc. When the full package is used, the external tools can be run out of the box.
The list of the external tools and their availability for different operating systems can be seen on this page.
For details about the system requirements see the corresponding chapter in the UGENE User Manual. For details about UGENE packages, see this page.
Customization and cooperation
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Commercial support
The commercial support includes bug-fixing on a priority basis, implementation of new features, and more. To know more, please contact us: [mailto:ugene@unipro.ru].