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-Wunsch alignme...2155 days ago
Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads
...etitive sequences. At last, Rainbow uses a greedy algorithm to locally assemble merged reads into contigs. Rainbow not only outputs the optimal but also suboptimal assembly results. Based on si...2033 days ago
EGAD: Ultra-fast functional analysis of gene networks
...haracterization across even thousands of functional groups to be accomplished in minutes in cross-validation and an analytic determination of the optimal prior to guess candidates gen...1977 days ago
HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
...rrection with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weig...1959 days ago
kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
...s existing tools. kallisto is described in detail in: Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter, Near-optimal probabilistic RNA-seq quantif...1953 days ago
DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
...omputes 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...1592 days ago
1215 days ago