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- BLAST, Smith-Waterman - popular basic local sequence alignment tools.
- HMMER2/HMMER3 - sequence analysis using profile hidden Markov Models constructed from multiple sequence alignments.
- ClustalW, ClustalO, Muscle, K-Align, Mafft, 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 REBASE database.
- Transcription factor binding sites analysis with SITECON, weight-matrix based algorithms and included version of JASPAR database.
- Short read aligners: BWA, Bowtie, Bowtie2, UGENE Aligner.
- GC-content, AT-content graphs.
- Mr bayes and Phylip tools for philogenetic phylogenetic trees construction.
- ... and dozens of other popular and highly cited tools.
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