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ADOMA stands for: Alternative Display Of Multiple Alignment. ADOMA can create four different displays of a multiple sequence alignment: a ClustalW alignment in HTML format, a simplified ClustalW alignment in HTML and/or txt format and a colored ClustalW alignment in HTML format. For examples of these outputfiles check the screenshots. ADOMA uses ClustalW to create the multiple alignment from DNA or protein sequences and displays them slightly different than the normal output of ClustalW. ADOMA is a commandline program that can easily be used in pipelines. For more information check the README.md in the Files section. How to cite ADOMA: Zaal, D. and Nota, B. (2016), ADOMA: A Command Line Tool to Modify ClustalW Multiple Alignment Output. Mol. Inf., 35: 42–44. doi: 10.1002/minf.201500083 http://onlinelibrary.wiley.com/doi/10.1002/minf.201500083/abstract
ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.
This library would be a collection of useful algorithm for math e physics programs. It will be developed in C language
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Using buildtemplateparallel.sh from ANTS on Condor
Virtual Image containing the ARMNLIB development environment and the GEM model from the Meteorological Research Division of the Canadian Meteorological Centre.
ARaC (Almost Random Cipher) is (or will become) a 512bit cipher. The ARaC suite is a C program which can encrypt/decrypt files and streams. The cipher itself cannot be download on SF due to US export laws, check http://arac-suite.sourceforge.net !
Novel Solexa (Illumina 1G) Base-Caller.
This library provides an Opensource ATPG API to build your programs on. The library implements a lot of template c++ classes and functions that provide Combitional/Sequential logic simulation, and fault simulation functionality(semi-PROOFS).2 weekly downloads
Provides auxiliary tools for the Monte Carlo particle transport code FLUKA (www.fluka.org).
Python, NLTK-based package for shallow parsing of Brazilian Portuguese15 weekly downloads
Affisix is a program for automatic recognition of prefixes. It takes large amount of words and according to the user setting it tries to determine which segments of these words are prefixes.
Aimgraph is a user-friendly front-end for the Atoms-In-Molecules analysis programs developed by Bader group.
Software to processing and analyze of airborne measurements.3 weekly downloads
A pipeline to define allele-specific genomic features2 weekly downloads
Alliance CAD System is a free set of EDA tools and portable cell libraries for VLSI design. It covers the design flow from VHDL up to layout. It includes VHDL simulator, RTL synthesis, place and route, netlist extractor, DRC, layout editor.11 weekly downloads
An open-source collection of materials for lectures, tutorials, labs, and software for a variety of primarily Computer Science courses. The materials include various course notes, presentation slides, source code samples, etc.
ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.5 weekly downloads
This project is aimed to the development of a framework for alife contests: the main rules of life, a graphical interface and some examples of elementary microorganisms (more complex survival strategies are developed by the contestants).
Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.
A framework for building distributed virtual reality applications, based on OpenGL|Performer(TM)
Bioinformatics Artificial Intelligence Order
BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.
shell scripts for MRI data processing
Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.2 weekly downloads