LSGSP is the java codes which provided for use on this site are not part of the book Large-Scale Genome Sequence Processing published by Imperial College Press
IGD (integrated genome database) is a method and tool for searching genome interval datasets more than three orders of magnitude faster than existing approaches, while using only one hundredth of the memory.
DupTree is a program for large-scale phylogenetic analyses using gene tree parsimony.The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses.
InterViewer is a software for visualizing large-scale protein interaction networks. InterViewer (1) first finds a layout of connected components of an entire network, (2) finds a global layout of nodes with respect to pivot nodes within a connected component, and (3) refines the local layout of each connected component by first relocating midnodes with respect to their cutvertices and direct neighbors of the cutvertices and then by relocating all nodes with respect to their neighbors within distance 2. Advantages of InterViewer over classical graph drawing methods include: (1) it is an order of magnitude faster, (2) it can directly visualize data from protein interaction databases, and (3) it provides several operations for effectively exploring large-scale protein interaction networks.
::DEVELOPER
Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon
phenomeImpute is an R package to impute missing values in large-scale high-dimensional phenome data. It includes several variations of KNN, random forest and MICE methods.
SNAVI (Signaling Networks Analysis and Visualization) is a Windows-based desktop application that implements standard network analysis methods to compute the clustering, connectivity distribution, and detection of network motifs, as well as provides means to visualize networks and network motifs. SNAVI is capable of generating linked web pages from network datasets loaded in text format. SNAVI can also create networks from lists of gene or protein names. SNAVI is a useful tool for analyzing, visualizing and sharing cell signaling data. SNAVI is open source free software.
MegaDot is a large scale dot plotter which is capable of producing dot density plots of tens of megabases of DNA sequence on a modest sized desktop machine, and of entire mammalian chromosomes on server scale computers.
MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
pymummer is Python3 module for running MUMmer and reading the output