Many-to-many pairwise alignments of two sequence sets
needleall reads a set of input sequences and compares them all to one or more sequences, writing their optimal global sequence alignments to file. It uses the Needleman-Wu...2140 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
Rainbow is developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. First, Rainbow clusters reads usi...2018 days ago
EGAD: Ultra-fast functional analysis of gene networks
With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficient tools to calculate functional properties in network...1962 days ago
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based o...1944 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...orms existing tools. kallisto is described in detail in: Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter, Near-optimal probabilistic RNA-seq quantif...1938 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
...s adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the...1577 days ago
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