DECIPHER (software)

DECIPHER is a software that can be used to decipher and manage biological sequences efficiently using the programming language R.

DECIPHER

Developer(s)	Erik Wright
Stable release	3.4.0 / 2025 (2025)
Written in	R, C
Operating system	Unix, Linux, macOS, Windows
Platform	x86-64, ARM
Available in	English
Type	Bioinformatics
License	GPL 3
Website	decipher.codes

Features

• Sequence databases: import, maintain, view, and export, and interact with a massive number of sequences.
• Homology finding: rapidly query sequences for homologous hits among a set of target sequences or genomes. Cluster into groups of related sequences.^[1]
• Multiple sequence alignment: align sequences of DNA, RNA,^[2] or amino acids.^[3]
• Genome alignment: find and align the syntenic regions of multiple genomes.
• Oligonucleotide design:^[4] primer design^[5][6] for polymerase chain reaction (PCR), probe design for fluorescence in situ hybridization (FISH)^[7] or DNA microarrays.^[8]
• Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes.
• Analyze sequences: find chimeras,^[9] detect repeats, predict secondary structure, classify into a taxonomy of organisms^[10] or functions,^[11] create phylogenetic trees, and ancestral reconstruction.
• Gene finding: predict coding and non-coding genes^[12] in a genome, extract them from the genome, and export them to a file.

See also

• Sequence alignment software