Search Results for "sql command line" - Page 29

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.

Alignment of the assembled sequences to a reference genome is a common way to obtain a likely order for the contigs, though most of times the final decision is taken by the user. We present the jContigSort, a tool that sorts the genome contigs.

This project is based on a personal effort for researches on dynamics of coevovling networks. As a physicist, I am trying to build a framework for discrete-time dynamics of general networks, and its software libraries with APIs.

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

SPINNEY provides an implementation of helicity spinors and related algorithms for the symbolical manipulation program FORM. The description of this package is published in http://arxiv.org/abs/1008.0803 .

This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text. The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...

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.

.... --- Highlights: --- org.knowceans.util: IndexQuickSort, TableList: apply order of one array/list to others +++ Vectors, ArrayUtils: array convenience +++ RandomSamplers, CokusRandom, ArmSampler, Densities: random sampling and distributions +++ Arguments: command line parser +++ StopWatch, Which, ExternalProcess: runtime stuff +++ ParallelFor: OpenMP workalike +++ PatternString, NamedGroupRegex: regex convenience --- org.knowceans.corpus: CorpusSearcher: full-text search engine +++ LabelNumCorpus: svmlight corpus storage and filtering +++ NIPS corpus with text, authors, labels and citations --- org.knowceans.map: InvertibleHashMultiMap, BijectiveHashMap: implement n:m and 1:1 relations. --- Other libs: knowceans-arms = port of the Adaptive Rejection Metropolis Sampler (ARMS) for arbitrary distributions +++ lda-j = port of lda-c, implementing Latent Dirichlet Allocation (LDA)

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

OpenBioGeoSim it's a open source software that simulates the stochastic origin and spread of species geographic ranges in a heterogeneous landscape. It's a free alternative based on Gary Entsminger's BioGeoSim.

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.

This project has been moved to https://github.com/loomchild/maligna . All further development will be done there.

SolSNP is a Java-based DNA variant calling tool for Next-Generation Sequencing alignment data. SolSNP uses a modified Kolmogorov-Smirnov statistic and data filtering to confidently and quickly call variants on high-coverage aligned genomes.

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.

Tidal Analysis Program in PYthon (TAPPY) uses the least squares optimization function from scipy to perform a harmonic analysis (calculate amplitude and phases of a set of sine waves) of a hourly time series of water level values.

The Wikipedia Miner toolkit provides simplified access to Wikipedia. This open encyclopedia represents a vast, constantly evolving multilingual database of concepts and semantic relations; a promising resource for nlp and related research.

PyEPL (Python Experiment-Programming Library) is a library for coding psychology experiments in Python. It supports presentation of both visual and auditory stimuli, and supports both manual (keyboard/joystick) and sound (microphone) input as responses.

GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.

RepMiner takes a graph theory approach to the classification and assembly of the repetitive fraction of genomic sequence data. Sequence lengths analyzed by RepMiner can range from full length transposable elements to low coverage sample sequence data.

JEuclid is a complete MathML rendering solution, consisting of: a MathViewer application, command line converters from MathML to other formats, an ant task for autmated conversion, display components for AWT and Swing and a component for Apache Cocoon

HanNanum is a Korean Morphological Analyzer and POS Tagger. A plug-in component-based architecture is adapted to the new Java version for flexible use. You can find the work flow for morphological analysis, POS tagging, noun extraction, etc. Contact: kschoi@kaist.ac.kr hjjeong@world.kaist.ac.kr

Set of iterative filters.

This open source software benchmarks the queries per second of an Apache Lucene index. It is an Java implementation and uses MultiFieldQueryParser to form a query.

jWords is a port of WORDS (by William Whitaker, a free latin-to-english dictionary program written in Ada), to Java. Besides the dictionary will be translated to the German language.

...The GUI plots the GPX track (latitude vs longitude) and lets the user remove GPS points from the beginning and end of the track respectively. There is also a built-in Command Line Interface. Note: No development anymore since I found out that GpsPrune does all the things I was looking for.