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Integrated Multiprogram Platform for Analyses in ConTest
Graphical User Interface for a software used to assess adaptive evolution in protein-coding genes. Makes use of several known bioinformatics software. IMPACT is free software, targeted to the scientific community.
Maldonado E, Dutheil JY, da Fonseca RR, Vasconcelos V, Antunes A (2011)
IMPACT: Integrated Multiprogram Platform for Analyses in ConTest.
Journal of Heredity, 102 (3): 366-369.
doi: https://doi.org/10.1093/jhered/esr003
Data curation tool to maintain variables for the National Survey of Health and Development managed by the Lifelong Health and Ageing Unit of the Medical Research Council.
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PAICE is a rapid bioinformatics pathway visualization tool for KEGG-compatible accessions derived from Illumina Solexa next-gen and Affymetrix datasets. It colors KEGG pathways while appreciating detection-calls and duplicate gene copies.
VELMA stands for Visualization & Exploration of Large Multiple sequence Alignments. VELMA is a Java tool for visualizing alignments of large numbers of biological sequences that exceed the capabilities of existing software.
The program versusSNP is a flexible tool for mining SNPs between two close related genomes. First, we align all the orthologous genes and select SNPs, then the SNPs are separated into categories based on their mutation types.
MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
3D Genome Tuner draws circular genome map and enables viewing multi-genomes in 3D context. It also provides genome analysis and sequence alignment, making it a powerful tool in genome studies and demonstrations.
Clinical study tracker tracks case study members through activities.
Developed at Medical Research Council UK to meet a common clinical trial need to track various types of clinical data. Users log dates of completed tasks against participant ID. Simple, useable, reduces lost data! Makes graphical progress reports.
A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.
The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html
RssGsc (Rank Sum Statistics for Gene Set Collections) is a bioinformatics tool used to find meaningful gene sets using a ranked list of genes (obtained form an experiment).
PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
GEAX is a Java application used to visualize and analyze cross-species gene expression microarray data.The program allows comparisons based on fold-change, p-value, quantile matching, or a combination of criteria.
TMAJ is software for Tissue MicroArrays (TMA's). Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program.
Executable program that measures sizes and other properties of colonies arrayed in a grid format (intended for 768, 384, or 96 colonies on agar plates) from jpeg images
The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.