A versatile pairwise aligner for genomic and spliced nucleotide sequences

Tools (written in C using htslib) for manipulating next-generation sequencing data

Toolkit for processing sequences in FASTA/Q formats

bedtools - the swiss army knife for genome arithmetic

De novo assembler for single molecule sequencing reads using repeat graphs

BWK awk modified for biological data

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

Sequence-to-graph mapper and graph generator

RAxML Next Generation: faster, easier-to-use and more flexible

GenomeTools genome analysis system.

Tandem Repeats Finder: a program to analyze DNA sequences

Nanopore data assembler

Find all significant local alignments between reads

A dotplot generator for large chromosomes

Integrated toolkit for analysis and evaluation of annotated genomes

tandem repeat finding from erroneous long reads

mdust from DFCI Gene Indices Software Tools (archived for a historical record only)

semi-automatic classification and postprocessing of LTR retrotransposons