Official GitHub repository:
- mrFAST: Read mapper developed
specifically for structural variation and segmental duplication
detection using the Illumina platform. Supports small indel
- mrsFAST: Similar to mrFAST, Hamming
- drFAST: Read mapper for di-base
color-space reads generated with the SOLiD platform.
- sirFAST: Read mapper for short
interrupted reads generated with the Complete Genomics platform.
Read depth analysis method to characterize segmental
duplications and predict absolute copy numbers.
Structural variation calling algorithm using read pair mapping
information including suboptimal alignments.
Detection of structural variants and indels from genome and
exome sequencing data.
Novel sequence insertion discovery framework.
Tool to efficiently compress FASTQ files.
Discover inversions using long range information.
Toolkit for automatic and rapid discovery of structural variants.
Discovery and genotyping of novel sequence insertions in many
- taveRNA suite
Algorithm that predicts the joint secondary structure of
two RNA sequences.
Densityfold algorithm that
minimizes a linear combination of energy density and the
total free energy.
RNA interaction search engine. pRuNA is a sequence based
pruning technique that eliminates a significant fraction of a non
coding RNA (ncRNA) data set and retains only the most likely ncRNA
candidates for forming a stable joint structure with the query
- piRNA: RNA-RNA interaction
partition function algorithm to predict the joint partition
function, equilibrium concentration, ensemble energy, and melting
temperature for two RNA sequences.
Novel ab initio
non-coding RNA finder.
A software tool that processes and manipulates multiple
alignments of genomic sequences.
An ab initio centromeric
sequence detection algorithm.