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TaxonFinder is an application that annotates taxon found in literature. The application harnesses a hybrid algorithm that is necessarily a combination of morphological analysis, dictionary lookup and Levenstein Distance algorithm.
t2prhd is a Perl script which generates simple diagrams that highlight relationships of sequence repeats detected by using a profile HMM in two sequences. Homology relations are identified on the basis of the phylogeny of repeats.
slclust: a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters.
The slclust utility is written in ANSI C++.
A library to process X-ray images from the Heimann imaging system. The XGray library has interfaces to C++ and Tcl and includes the graphical program XRayLab, which is written Tcl.
OpenDMAP (Open Source Direct Memory Access Parser) is a natural language processing (text mining) application: a semantic parser for information extraction.
This Python 3.1 tool manipulates the coordinate system of CNC GCODE for machining or engraving. It can Flip X, Y, or Z coordinates, mirror X, Y, or Z coordinates, flip or Mirror both XY coordinates, or insert Z motions into a GCODE file devoid of them.
HOT is a package of Matlab and Octave compatible functions that manage thermodynamic data for a wide range of species. Functions calculate almost all the most common thermodynamic quantities of mixtures.
Python users may also want to look at PYroMat at https://chmarti1.github.io/PYroMat/index.html
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AnnaF is an automatic gene annotation framework, that is used to do some automatic annotation for C. higginsianum. It was also tested on F. graminearum and should work well for fungi in general.
AnnaF was build upon the pipeline framework Anna.
* Java classes for parsing text, conversion to XML or to evaluate in Java. The parser is textual-script-controlled with a syntax near Backus Naur Format, named ZBNF. * Some routines for conversion: C-Header or Java to XMI, XML-Documentation generation,
RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats.
Radar has moved to github (https://github.com/AndreasHeger/radar)
BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
A cross-platform library that computes fast and accurate SIFT image features. libsiftfast provides Octave/Matlab scripts, a commandline interface, and a python interface (siftfastpy). Optimized with SIMD instructions and OpenMP .
Maximally flat (maxflat) digital filter design in Java, with arbitrary numbers of poles and zeros. "Maximally flat" means that the magnitude frequency response has the maximum number of vanishing derivatives at 0 and pi.
On December 8, 2009 the UK Met Office released records of worldwide land surface temperature readings. This project analyzes these records and produces output files that can be read by gnuplot and Google Earth to show temperature trends.
Converts Digital Terrain Elevation Data from one level to another. (Currently only converts DTED1>DTED2) No longer in development due to personal time constraints. If there are features you desperately need, feel free to ask, or write it your self :)
This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.
Avenzoar is a one-year exploration of renal cell carcinoma morphology and its related single nucleotide polymorphisms (SNPa) as a method of automating diagnosis of cancer by using a computer-aided decision tree controlled by analytical statistics.
Maximally flat (maxflat) digital filter design for Octave and Matlab. "Maximally flat" means that the magnitude frequency response has the maximum number of vanishing derivatives at 0 and pi. Handles arbitrary numbers of poles and zeros.