DECIPHER - Home (original) (raw)

Overview

DECIPHER is a software that can be used for deciphering and managing biological sequences efficiently in the R programming language. The R package is distributed as platform independent source code under the GPL version 3 license.

Installation

To install DECIPHER, start the latest version of R and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("DECIPHER")

Visit the Tutorials page to learn how you can get started DECIPHERing. Questions can be posted on the Bioconductor Support forum or contact us.

Features

• Sequence databases: import, maintain, view, export, and interact with a massive number of sequences.
• Analyze sequences: classify into a taxonomy of organisms or functions, detect repeats, find chimeras, predict secondary structure, create phylogenetic trees, and reconstruct ancestral states.
• Manipulate sequences: trim low quality regions, correct frameshifts, reorient nucleotides, determine consensus, or digest with restriction enzymes.
• Sequence alignment: accurately align thousands of DNA, RNA, or amino acid sequences. Quickly find and align the syntenic regions of multiple genomes.
• Homology finding: rapidly query sequences for homologous hits among a set of target sequences or genomes. Cluster into groups of related sequences.
• Population genetics: infer demography, infer recombination, and infer selection.
• Gene finding: predict coding and non-coding genes in a genome, extract them from the genome, and export them to a file.
• Oligo design: test oligos in silico, or create new primer and probe sequences optimized for a variety of objectives.