Search Results for "java open source" - Page 40

OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.

Febrl (Freely Extensible Biomedical Record Linkage) does data standardisation (segmentation and cleaning) and probabilistic record linkage ("fuzzy" matching) of one or more files or data sources which do not share a unique record key or identifier.

BIGrat: a genome assembly tool for pyrosequencing-based re-sequencing

PerlPrimer is a GUI application written in Perl that designs primers for standard PCR, bisulphite PCR and Real-time PCR (QPCR). It aims to automate and simplify the process of primer design.

Displays mummer/nucmer mappings and prints PNG to stdout via the "show-coords -lcdTH" output. The output file is <coords-output>.png. Command line options allow for different features when producing the image. Within the code there are comment blocks which give examples of how to further customize it i.e. grouping based on name similarity, color, etc. This program is aimed at providing full customization within the limits of the Bio-Graphics module. Current version supported is Bio-Graphics-2.25

ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.

Diva is a command-line tool for dispersal-vicariance analysis, a simple method for inferring the distributional history of organisms (Ronquist, F. 1997. Systematic Biology 46:193-201).

Software for parsimony-based tree fitting, which can be used for analysis of problems in historical biogeography, coevolution, and in species tree - gene tree fitting.

A fast efficient way of dealing with large amounts of Blast or Repeatmasker data.

A bioinformatics tool to identify and remove rRNA sequences from metagenomic and metatranscriptomic datasets. The rRNA-like sequences are classified by domain, subunit. and bacterial phyla. Coverage plots for the top hits are provided as well.

Shrec is a bioinformatics tool for error correction of HTS read data.

A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions

We present an improved ball and stick representation called HyperBalls. This type of depiction is particularly useful to represent dynamic phenomena, such as the evolution of non covalent bonds and takes advantage of GPU capabilities. HyperBalls are now fully integrated into the UnityMol software and are actively developed in that context. You will find the most up-to-date versions of the shaders in the http://unitymol.sourceforge.net project.

PyBact is an open source software written in Python for Bacterial Identification. The software generates simulated data matrix which accurately represents the probabilistic positive/negative results of the tested biochemical test.

SimBac is a software package for simulating bacterial genome evolution. It outputs samples of DNA sequences at each generation & allows testing of major evolutionary mechanisms, including mutation, recombination, genetic drift, and natural selection.

BpMatch is an algorithm that, given 2 strings S and T, compute the maximum coverage of T using only subequence or reversed complemented subsequences of S, of minimum length l.

BFAST facilitates the fast and accurate mapping of short reads to reference sequences, where mapping billions of short reads with variants is of utmost importance.

The project would include the development of XUL, CSS and Javascript components to assist biologists in sequence manipulations, data mining, data analysis, etc.).

iso2l (ˈaisəutuːl, spoken isotool) is a software to calculate the isotopic distribution of a chemical formula or a amino acid chain. The development has been MOVED TO https://github.com/binfalse/iso2l

PHACCS is a bioinformatic tool designed for a scientific public. It gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.

SVGMap is an open source web tool to help you in the visualisation of experimental data associated to some graphical representation. More at : 1. Project website http://bg.upf.edu/svgmap 2. Reference : Xavier Rafael-Palou, Michael P. Schroeder, and Nuria Lopez-Bigas SVGMap: configurable image browser for experimental data Bioinformatics 2011 : btr581v1-btr581.

Diversity Maps is a data visualization tool for plant geneticists and breeders. It generates publication-quality, vector-based chromosome maps displaying differences in marker states between individuals.

This is a Python program based on the NegEx algorithm that detects the polarity of the clinical evidence in clinical random trials. If you use this code please cite this paper: P. Davis-Desmond and Diego Mollá. Detection of Evidence in Clinical Research Papers (2012). Australasian Workshop On Health Informatics and Knowledge Management (HIKM 2012), Melbourne, Australia. http://www.ics.mq.edu.au/~diego/publications/hikm12.pdf

The Parenthesis Classifier takes the contents of a set of parentheses and classifies it into one of several categories. It includes a parenthesized-data extractor and the classifier.

Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. Suitable for mammalian repertoire sequences obtained either by Sanger or 454 sequencing. Methods published in Glanville, Zhai, Berka et al, PNAS 2009.