Search Results for "java terminal emulator"

This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and...

ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.

NOTE: Project moved to https://github.com/MolBIFFM/PTGLtools. The Visualization of Protein-Ligand Graphs (VPLG) software package computes and visualizes protein graphs. It works on the super-secondary structure level and uses the atom coordinates from PDB files and the SSE assignments of the DSSP algorithm. VPLG is command line software. If you do not like typing commands, try our PTGL web server: http://ptgl.uni-frankfurt.de/

The Integrated Analysis Platform (IAP) has been designed and developed to support the analysis of large-scale image data sets of different camera systems. It aims in bridging different data domains and in integrating different approaches to data analysis and post-processing.

openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.

JGAP is a Genetic Algorithms and Genetic Programming package written in Java. It is designed to require minimum effort to use, but is also designed to be highly modular. JGAP features grid functionality and a lot of examples. Many unit tests included. Legal notice/Impressum: Klaus Meffert An der Struth 25 D-65510 Idstein sourceforge <at> klausmeffert.de

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.

cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments.

Darwin 2: Java Framework for Evolutionary Computation (genetic algorithm, GA). A true framework with out-of-the-box functionality and extensibility of all classes. Interface-based pattern with dependency-injection to configure components.

Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files

iPiG targets the integration of peptide spectrum matches (PSMs) from mass spectrometry (MS) peptide identifications into genomic visualisations provided by genome browser such as the UCSC genome browser (http://genome.ucsc.edu/). iPiG takes PSMs from the MS standard format mzIdentML (*.mzid) or in text format and provides results in genome track formats (BED and GFF3 files), which can be easily imported into genome browsers. For more details about iPiG and it's functionallity, please...

GenoGUARD is a DNA sequence screening software that implements the best match method recommended by the federal government to detect the presence of biosecurity threats in synthetic DNA orders.

A simple tool to import the diff, gtf and tracking files from cufflinks, cuffcompare, cuffdiff into a new sqlite database for data mining.

BorderFlow implements a general-purpose graph clustering algorithm. It maximizes the inner to outer flow ratio from the border of each cluster to the rest of the graph.

Grid-Enabled Molecular Simulation Repository (GEMS)

Java API for implementing any kind of Genetic Algorithm and Genetic Programming applications quickly and easily. Contains a wide range of ready-to-use GA and GP algorithms and operators to be plugged-in or extended. Includes Tutorials and Examples.

Large set of functions for biological records (ECG, EEG, phono), datastore, datamining and analysis (HRV, QT, RR, ST). The application is written in Java, so that it is assumed to work on all devices. It runs as a desktop or client-server application. It

FORce based Cluster Editing (FORCE) is a Java software heuristically solving the graph cluster editing problem on weighted edges using BLAST E-values. It further provides a training mode for heuristic parameter estimation.

neochip is a collection of algorithms for high-density oligonucleotide microarrays. The current version contains heuristic algorithms that attempt to improve the quality of arrays by re-designing their layout (the location of the probes on the chip).

NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.

A biological data warehouse that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. Website: http://bioinformatics.ubc.ca/atlas