Documentation

DECIPHER is a software toolset that can be used to maintain, analyze, and decipher large amounts of DNA sequencedata. To install DECIPHER, see the Downloads page.

To begin using DECIPHER read the "Getting Started DECIPHERing" tutorial. Refer to the PDF documents below for instructions on how to use DECIPHER for various tasks.

	Reference Manual
	Getting Started DECIPHERing
	The Art of Multiple Sequence Alignment in R
	Classify Sequences in R
	Design Microarray Probes in R
	Design Group-Specific Primers in R
	Design Group-Specific FISH Probes in R
	Design Primers that Yield Group-Specific Signatures
	Detecting Obscure Tandem Repeats in Sequences
	The Double Life of RNA: Uncovering Non-Coding RNAs
	Finding Chimeric Sequences in R
	Growing Phylogentic Trees in R with Treeline
	Population Genetics Inference in R
	The Magic of Gene Finding
	Searching Biological Sequences for Research
	Upsize Your Clustering with Clusterize