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
MR-MSPOLYGRAPH is a MapReduce based implementation for parallelizing peptide identification from mass spectrometry data
MSPolygraph is an open source hybrid database and spectral library MS/MS search engine that runs in either serial or parallel modes. MSPolygraph examines the ions in MS/MS spectra to identify likely matching candidate peptides from a reference database of protein sequences (.Fasta file). MSPolygraph also supports searching a spectral library (collection of annotated MS/MS spectra).
pGraph /psgraph (parallel sequence graph construction) is a novel hybrid between the hierarchical multiple-master/worker model and producer-consumer model, and is designed to break the irregularities imposed by alignment computation and work generation.
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.
Serena G. Liao&, Yan Lin&, Dongwan Kang, Naftali Kaminski, Frank C. Sciurba, George C. Tseng. (2014)
Missing value imputation in high-dimensional phenomic data: Imputable or not? And how?.