SuperLU is a library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. It comes in two different flavors: SuperLU_MT (multithreaded) for shared memory parallel machines and SuperLU_DIST for distributed memory parallel machines.
TurboVNC is an implementation of VNC optimized for 3D graphics rendering. Like other VNC software, TurboVNC can be used to create a virtual desktop on a remote machine, which can be useful for visualizing CPU-intensive graphics produced remotely.
The Visualization ToolKit (VTK) is an open source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java and Python.
TotalView is a symbolic debugger which supports threads, MPI, OpenMP, C/C++ and Fortran, plus mixed-language codes. Advanced features include on-demand memory leak detection, heap allocation debugging and the Standard Template Library Viewer (STLView). Other features like dive, a wide variety of breakpoints, the Message Queue Graph/Visualizer, powerful data analysis and control at the thread level give you the power you need to solve tough problems.
Gnuplot is a portable command-line driven data and function plotting utility. It was originally intended to allow scientists and students to visualize mathematical functions and data.
"RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program." (http://www.repeatmasker.org/)
"TreeBeST is an original tree builder for constrained neighbour-joining and tree merge, an efficient tool capable of duplication/loss/ortholog inference, and a versatile program facili- tating many tree-building routines, such as tree rooting, alignment filtering and tree plot- ting. TreeBeST stands for ‚Äò(gene) Tree Building guided by Species Tree‚Äô. It is previously known as NJTREE as the first piece of codes of this project aimed to build a eighbour-joining tree.
TreeBeST is the core engine of TreeFam (Tree Families Database) project initiated by Richard Durbin. The basic idea of this project is to build a full tree constrained by a manually verified seed tree. The tree builder must know how to utilize the prior knowledge provided by human experts. This demand disqualifies any existing softwares. Given this fact, we devised a new algorithm to control the joining step of traditional neighbour-joining. This is origin the constrained neighbour-joining.
When trees are built, they are only meaningful to biologists. Computers generate trees, but they do not understand them. To understand gene trees, a computer must be equipped with some biological knowledges, the species tree. It will teach a computer how to discriminate a speciation from a duplication event and how to find orthologs, provided a correct gene tree.
Unfortunately, gene trees are not always correct. Since the advent of UPGMA algorithm in 1958, we have tried to find a ideal model for nearly half a century. But we failed. Evolution is so complex a thing. A model best fits in one lineage might mean a disaster in another. A unified model is far from being discovered. TreeBeST aims at improving the accuracy of tree building, but it does not try to set up a new model in a traditional way. Instead, it integrates two existing models with the help of species tree, finding the subtree that best fits the models and merging them together to build a new tree incorporating the advantages of the both. This is the tree algorithm." (treebest.pdf)
“Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes.” (http://selab.janelia.org/recon.html)
"RAxML is a fast implementation of maximum-likelihood (ML) phylogeny estimation that operates on both nucleotide and protein sequence alignments."
mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. mpiBLAST takes advantage of distributed computational resources, i.e., a cluster, through explicit MPI communication and thereby utilizes all available resources unlike standard NCBI BLAST which can only take advantage of shared-memory multi-processors (SMPs).