DECIPHER (software)
DECIPHER is a software toolset that can be used to decipher and manage biological sequences efficiently using the programming language R. Some functions of the program are accessible online through web tools.Features
- Sequence databases: import, maintain, view, and export sequences.
- Multiple sequence alignment: align sequences of DNA, RNA, or amino acids.
- Genome alignment: find and align the syntenic regions of multiple genomes.
- Oligonucleotide design: primer design for polymerase chain reaction, probe design for fluorescence in situ hybridization or DNA microarrays.
- Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes.
- Analyze sequences: find chimeras, predict secondary structure, classify into a taxonomy,, create phylogenetic trees, and ancestral reconstruction.
