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ANTLR (ANother Tool for Language Recognition) is a powerful parser generator for reading, processing, executing, or translating structured text or binary files.
Jitsi is an audio/video and chat communicator that supports protocols such as SIP, XMPP/Jabber, IRC and many other useful features.
An extremely easy way to perform background processing in Java. Backed by persistent storage. Open and free for commercial use.
Implementation of various string similarity and distance algorithms: Levenshtein, Jaro-winkler, n-Gram, Q-Gram, Jaccard index, Longest Common Subsequence edit distance, cosine similarity ...
Apache MINA sshd is a comprehensive Java library for client- and server-side SSH.
Apache Wicket - Component-based Java web framework
An open-source Java library for Constraint Programming
A fast, lightweight Java library for creating Scalable Vector Graphics (SVG) output.
Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository
New Genome Browser (NGB) - a Web - based NGS data viewer with unique Structural Variations (SVs) visualization capabilities, high performance, scalability, and cloud data support
Modular and modern graph-theory algorithms framework in Java
SVG diagrams generation: single-line substation diagrams and network graph diagrams
Small java command line utility to unlock pdf files (remove any copy/edit/print protections)
High throughput protein function annotation with Human Readable Description (HRDs) and Gene Ontology (GO) Terms.
iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. It is capable of importing and exporting models specified using the Systems Biology M…
TaxTriage is a Nextflow workflow designed to agnostically identify and classify microbial organisms within short- or long-read metagenomic NGS data. This flexible tool was developed with various us…
BBTools: Official suite of fast, multithreaded bioinformatics tools for DNA/RNA analysis. BBMap aligner, BBDuk trimmer, BBMerge, and 90+ other tools. Actively maintained by Brian Bushnell.
Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC) Metagenome Assembler
Multithreaded Gephi Force Atlas2 Layout in 2 or 3-d
180+ Java applications for analyzing next generation sequencing data from ChIPSeq, RNASeq, BisSeq, DNASeq, variant annotation/ filtering, alignment/VCF QC, capture array design, IGV/ DAS2/IGB/UCSC …
A Java implementation of the Anaerobic Digestion Model No 1 (ADM1) with modifications