2229 days ago
Jvarkit : Java utilities for Bioinformatics
Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics2172 days ago
CGView - Circular Genome Viewer
CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as...2160 days ago
GFinisher: a new strategy to refine and finish bacterial genome assemblies
...prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar GenomeFini...2124 days ago
Qualimap2: Evaluating next generation sequencing alignment data
Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality...2077 days ago
MimicrEE2: Genome-wide forward simulations of Evolve and Resequencing studies
MimicrEE2, a multi-threaded Java program for genome-wide forward simulations of evolving populations. Mim...s, polygenic adaptation, epistasis). MimicrEE2 runs on any computer with Java installed. It is distributed...2060 days ago
CSBFinder: Discovery of colinear syntenic blocks across thousands of prokaryotic genomes
CSBFinder is a standalone Desktop java application with a graphical user interface, that can also be executed via command line. CSBFinder implements a novel methodology for the disc...2034 days ago
BamView: a free interactive display of read alignments in BAM data files
...NIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and...mand line options are given when '-h' is used: java -jar BamView.jar -h BAM file...fied on the command line with the '-a' option: java -mx512m -jar BamView.jar -a p...2018 days ago
molinspiration: broad range of cheminformatics software tools supporting molecule manipulation
...hes. Our products support also fragment-based virtual screening, bioactivity prediction and data visualization. Molinspiration tools are written in Java, therefore can be used practi...1946 days ago
Osprey: Network Visualization System
...Osprey is developed by the TyersLab and is a part of the BioGRID family of software. It utilizes both MySQL and Java to operate and is compat...1946 days ago