Py_ContigViewer is a contig viewer, a stand alone cross-platform desktop application that uses CAP3 alignments to graphically display and validate candidate SNPs and InDels. It also simplifies PCR oligo design in an interactive mode. The extended mode provides the display of BLAST hits of annotated sequences with intron positions for the selected contig. Py_ContigViewer works in conjunction with DIS (Deletion, Insertion, Substitution) SNP discovery pipeline at http://www.atgc.org/SNP_Discovery/.
Vigyaan is an electronic workbench for bioinformatics, computational biology, and computational chemistry. It is a Linux-live CD containing all the required software to boot the computer with ready to use modeling software. It includes Artemis, Bioperl, BLAST (NCBI-tools), ClustalX, Cn3D, EMBOSS tools, Garlic, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, JMol, MPQC, NJPlot, Open Babel, Octave, PSI3, PyMOL, Rasmol, Raster3D, SMILE, TINKER, XDrawChem, Xmgr, and Xfig.
ProActive is a Java library for parallel, distributed, and concurrent computing as well as mobility and security in a uniform framework. It provides a comprehensive API and a graphical interface and is based on an Active Object pattern, a uniform way to encapsulate a remotely accessible object, a thread as an asynchronous activity, an actor with its own script, a server of incoming requests, a mobile and secure agent, and a component with server and client interfaces. It simplifies the programming of applications distributed over a LAN, clusters, an intranet, or Internet GRIDs.
CoaSim is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It efficiently constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on the states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.
MCL-edge is an integrated command-line driven workbench for large scale network analysis. It includes programs for the computation of shortest paths, diameter, clustering coefficient, betweenness centrality, and network shuffles. A module for loading and analyzing gene expression data as a network is provided. The MCL algorithm is a fast and highly scalable cluster algorithm for networks based on stochastic flow. The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure, which is revealed as the imprint left by the process. The threaded implementation has handled networks with millions of nodes within hours and is widely used in the fields of bioinformatics, graph clustering, and network analysis.
FinchTV is a way to easily view and edit your DNA sequencer chromatogram data. It can display an entire trace in a scalable multi-pane view, and will also display quality values (when available). You can edit your base calls and save your data to a new chromatogram file for later use, select and copy sequence for use in other applications, and print your trace out to paper or a file. You also have the ability to search your sequence data using regular expressions or simple base queries, to view raw data from .ab1 files, and to reverse complement your sequence and traces.