2012 March
- VISDA – Visualization, and Discovery for Cluster Analysis of Genomic data
- DDN – Identify Condition-specific Topological Changes in Biological Networks
- COCA – Knowledge-guided Gene Ranking
- mSD – Regulatory Module Identification
- ml-SVR – Identify Condition-Specific Regulatory Networks
- CNSuite – caBIG Analytical Tool for Copy Number analysis
- BACOM 1.0 – Bayesian Analysis of COpy number Mixtures
- BMRF – Pathway Network Identification
- MECPM – Maximum Entropy Conditional Probability Moldeling
- Synthesis-View – Visualization and Interpretation of SNP Association Results
- MdrPDT 2.0.1.21 – Multifactor Dimensionality Reduction and genotype Pedigree Disequilibrium Test
- genomeSIMLA 1.1.1 – Forward-time Population Simulation
- ATHENA 1.0 – Discover Epistasis among Quantitative Trait Loci
- MDR 2.0 – Multifactor Dimensionality Reduction
- GenoPlayer 20070621 – Visualizing and Querying Genetic Data
- MapPop 1.0 – Software for Selective Mapping and Bin Mapping
- eQTNMiner 2.0.0 – High-resolution Mapping of Quantitative Trait Loci
- MetaQTL 1.2.0 – Meta-analysis of QTL Mapping Experiments
- SAP 1.0.12 – Statistical Assignmnet Package
- MDBLOCKS 1.0 – Minimum Description length method for Haplotype BLOCKS
- DarwinXporter 0.1.3 – Export Diversity Analysis data for Darwin from Excel data sheets
- DARwin 5.0.158 – Diversity and Phylogenetic Analysis
- cM Converter – Convert in Batch Physical to Genetical Map Positions of Molecular Markers of Rice
- CIST – Analysis of Gene Expression data Generated using SAGE
- MANTEL-STRUCT 1.0 – Tests for Population Structure through the use of Mantel Tests
- TFPGA 1.3 – Analysis of Allozyme and Molecular Population Genetic data
- AIS 1.0 – Joint Analysis of Inter-individual Spatial and Genetic Information
- Pajek Writer – Generation of Structural Representation of Biochemical Processes in Format Pajek
- GeneNetStudio 2011 – Visual Reconstruction and Analysis of Network Models of Molecular-genetic Systems
- FermentVelocity – Generation of Enzymatic Reaction Velocity Equations
- MQscore 1.0 / MQscore_SNP 1.1 – Parametric Linkage analysis of Quantitative Traits in large pedigrees
- PedPeel 0.0.2 – Prepare Pedigree data for Calculation of Elston-Stewarts’ Likelihood function
- PedigreeQuery 20080410 – Drawing Pedigrees step-by-step
- MGA-SIMULATE – Simulation of Genotypes and Quantiative Phenotyps
- MGA-MAPF 2 – Map QTL in Model Organisms using a data coming from Backcrosses
- MAN-A1 – Complex Segregation Analysis in Humans
- MAIA 1.0 – Complex Segregaton Analysis in Animal Pedigrees
- Shuffle 1.02 – Shuffle a DNA Sequence Any Number of Times
- Madeline 2.0 – Pedigree Drawing Engine
- Willows 1.1 – Tree and Forest Construction package
- Twin Analysis – Twin Analysis Using SAS
- STREE – Survival Analysis Trees
- RTREE – Classification Trees for Risk Profile and Diagnosis
- MASAL – Multivariate Adaptive Splines for Analysis of Longitudinal Data
- HapForest – Forest for Detecting Haplotypes and Interactions
- CTMBR – Classfication Trees for Multiple Binary Responses
- AAOT — Association Analysis of an Ordinal Trait
- LOT 1.2 – Linkage Analysis of Ordinal Traits
- MiniInbred 2.0 – Calculate and Minimize Inbreeding Coefficients
- Pedigraph 2.4 – Draw Pedigrees
- SPSSQTL 1.0 – Statistical Power and Sample Size for QTL Detection
- EPISNPmpi 4.2 / epiSNP 4.2 – Epistasis Testing in Genome-wide Association Studies
- SNPEVG 2.1 – SNP Effect Viewing and Graphing
- LOCUSMAP 1.1 – Rapid Linkage Analysis and Map Construction of Loci
- sequtils 0.2.7 -software for Sequence Manipulation
- LEA / parLEA – Likelihood-based Estimation of Admixture
- MEDUSA – Motif Element Detection Using Sequence Agglomeration
- VISTAL – Two-dimensional Visualization tool for Structural Alignments
- SURFace – Calculate Solvent accessible surface area
- intf_model – Protein-DNA Modeling Interface
- Protein-DNA Interface Alignment – Interface Alignment between any Two Protein-DNA complexes
- PrISM – Protein Informatics System for Modeling
- Jackal 1.5 – Protein Structure Modeling Package
- GRASP 2 -Visualization of Macromolecular Structures and Sequences
- SILACtor 1.0 – Dynamic SILAC studies
- BLinks 2.0 – Software for PIR Technology
- FT-ARM – Identification and Quantification of Multiplexed High-resolution
- NetSeed – Identify the Seed sets of Networks
- Hardklör 1.36 – Analysis of High- resolution Mass Spectra
- IDCalc 0.3 – Isotope Distribution Calculator
- GPCRHMM – GPCR detection method
- EMMA 1.1.2 – Efficient Mixed-Model Association
- Strut 0.1 – Protein Function Prediction
- Fido – MS/MS Protein ID Software
- Segtools 1.1.9 – Provide Exploratory data Analysis on Genomic Segmentations
- Genomedata 1.3.2 – Storage of Multiple Tracks of Numeric data Anchored to Genome
- Philius – Predict Protein Transmembrane Topology and Signal Peptides
- Pythia 1.0.1 – Thermodynamically based PCR primer design program
- HMMSeg – Scale-specific Segmention of Continuous Genomic data using HMMs
- Percolator 2.04 – Confident Peptide Identifications from a collection of Tandem Mass Spectra
- hyfi – software suite for Binding Site Search
- BiblioSpec 2.0 – Creat and Search MS/MS Peptide Spectrum Libraries
- Cleaner 1.03 – Assembly of Informative, Transcript-specific Probe-clusters
- MINDY 2 – Genome-wide Discovery of Modulators of Transcriptional Interactions
- ARACNE 2 – Reconstruction of Accurate Cellular Networks
- Rankprop – Protein Ranking by Network Propagation
- ErmineJ 2.1.21 – Analysis of Gene sets in Expression Microarray data
- Gemma 1.5 – Analyze Genomics data using Meta-analysis
- matrix2png 1.2.2 – Visualization tool for Display of Matrix data
- Segway 1.1.0 – a way to Segment the Genome
- ldgroup – Linkage Disequilibrium Grouping of SNPs
- LAPSTRUCT 1.0 – Geometric Approach to Describe Population Structure
- KNNimpute – Estimation of Missing Values in Microarray data
- ChARMview 1.8 – Visualization-based Discovery and Analysis of Genomic Abberations in Microarray data
- MEFIT – Microarray Experiment Functional Integration Technology
- NNN 1.01 – Nearest Neighbor Networks Clustering
- Sleipnir 3.0 – Sleipnir Library for Computational Functional Genomics
- mouseMAP – Tissue-specific Functional Networks for the Laboratory Mouse
- TEAM 0.0.4 – Two-locus Epistasis tests in human Genome-wide Association Study
- COE 0.0.5 – Genome-Wide Two-Locus Epistasis Test in Disease Association Study
- FastANOVA 0.0.5 – Perform ANOVA Tests on SNP-pairs in Batch mode
- SNPbrowser 4.0 – Analyze and Visualize the Immense SNP Datasets
- NPUTE – Data Structure for Finding Pair-wise Haplotype Similarity
- HiDimViewer – Visualization tool for High-dimensional Datasets
- VLAD 1.5.1 – Visualize GO Annotations
- Pseudomarker 2.04 – Analysis of QTL data from Inbred Line Crosses
- phylo 0.3 – Phylogenetic Tree Viewer
- WCluster – Weighted Hierarchical Clustering
- HIDRA 1.1.1 – Multi-dataset Microarray Visualization System
- geneVAnD 1.0 – Visualization of Statistical Snalysis of Microarray Clusters
- GOLEM 2.1 – Graph-based Gene-ontology Navigation and Analysis tool
- MouseDivGeno 1.0.4 – Genotype the Mouse Diversity Genotyping Array
- PubArray 1.0.0 – Turn Analyzed Results of Microarray Experiment into Web Application
- J/maanova 1.1.1 – Java GUI for R/maanova
- R/maanova 1.16.0 – Environment for Microarray Analysis
- MapQTL® 6 – Mapping of Quantitative Trait Loci in Experimental Populations of Diploid Species
- JOINMAP 4.1 – Calculation of Genetic Linkage Maps
- Celestial3D 1.0.1 – Graphical Display of Familial Information
- SimHap 1.0.2 – Haplotypic Analysis of Population-based data
- JLIN 1.6.0 – Visualisation of LD Analysis
- MLDA 2.0 – Methylation Linear Discriminant Analysis
- CHROMOWAVE 1.0 – Microarrays Data Analysis
- XperimentR – Ease the pain of Annotating Biological Experiments and Laboratory Processes
- BVS – Matlab toolbox for Bayesian logistic and Probit Regression
- ESS++ 0.1.0 – Bayesian Variable selection for Linear Regression using Evolutionary Monte Carlo
- Gmix – Bayesian Analysis of Univariate Normal Mixtures
- BGmix 1.0.0 – Bayesian Mixture Model for Differential Expression
- fuzzyFDR 1.0 – Find Fuzzy Decision Rules for Multiple Testing of Hypotheses with Discrete data
- LDtests 1.0 – Tests of Linkage Disequilibrium and Hardy-Weinberg Equilibrium
- FREGENE – Aimulate Sequence-like data in large Genomic Regions and large Populations
- HyperLasso – Simultaneous analysis of GWAs
- invertFREGENE – Simulate Sequence Level data with Inversions
- metaMapper 1.01 – Meta-analysis program for Genome-wide Association
- AncesHC 2009 – Association Tests by Inferring Ancestral Haplotypes using a Hidden Markov Model
- polyHap 2 – Phase Polyploids and Copy Number Regions
- cnvHap 1.033 – Joint Copy Number Genotyping
- convertimpute – Convert IMPUTE format to MultiPhen format
- cnvPipe 0.82 – Enable CNV Meta Analysis
- cnvHiTSeq – Detect and Genotype CNVs in WGS data
- famCNV 1.0 – Copy Number Variant Association for Quantitative Traits in Families
- JENTI 2008 – Mine Complex Inbred Genealogies
- Mask – Mask bad Probes in Affymetrix Expression data
- PTS 1.0.2 – Parallel Tagged Sequencing
- PatMaN 1.2.2 – DNA Pattern Matcher for Short Sequences
- ANFO 0.98 – Mpper for Ancient DNA
- neuroants – Simulation of Ant Colony
- mega_nexus 1.0 – Convert MEGA input files to Splitstree input files
- ASJPdates 1.1 – Calculate ASJP dates
- ASJPSoftware 2.1 – Calculate ASJP Distance Matrices
- NewickReader 1.0 – Produce Distance Matrix from Branch Lengths in Phylogenetic Tree
- DistanceCorrelations 1.0 – Correlate Data Matrix with Branch Lengths of Phylogenetic Tree
- AlgorithmTreeFromLabels 1.0 – Creat Nexus files from Classificatory Language labels
- Polymorph 1.0.0 – Determine Allele and Polymorphism Frequencies in MLST datasets
- Sequence Comparator 2.0.1 – Compares a Query Sequence with Known Sequences
- ProfCheck 0.9.0 – Check the Integrity of MLST data-sets
- CodonW 1.4.4 – Codon Usage Analysis
- AgdbNet 1.0.4 – Antigen Sequence database software for Web-based Bacterial Typing
- START2 – Sequence Type Analysis and Recombinational Tests
- SimMLST 1.0 – Simulation of MLST data under a Neutral Model
- xmfa2struct – Converts files in eXtended Multi-Fasta format into Structure file
- GenoPlast 1.0 – Bayesian Analysis of Genome Plasticity
- ClonalFrame 1.2 – Inference of Bacterial Microevolution using Multilocus Sequence data
- ClonalOrigin – Recombination Detection in Bacteria
- sequenceLDhot – Hotspot Detection
- sequenceLD – Approximate Likelihood
- Genetree 9.0 – Software for Ancestral Inference.
- HOTEL_FAM 0.3 – Calculate Hotelling’s T2 Statistic for data of nuclear families
- HOTEL_CC 0.1 – Calculate Hotelling’s T2 Statistic for Case-control data
- TDTPOWER 1.0b – Note on Power Approximations for TDT
- RC-TDT 1.1d – Reconstruction-combined Transmission Disequilibrium Test
- ILR 2.2 – Imprinting Likelihood Ratio
- PEDIGREE-EXPLORER 2.0 – Explore Pedigree
- FAMHAP 19 beta – Haplotype Association Analysis Software
- INTERSNP 1.0.10 – Genome-wide Association and INTERaction Analysis of SNP
- MolFit 2 – Protein-Protein docking Program
- mDraw 1.0 – Network Visualization Tool
- mfinder 1.2 – Network Motifs Detection tool
- MetaboQC 1.0 – Evaluation of peak picking quality in LC-MS Metabolomics data
- RNAmotifs 3 – Predict a motif for your own set of RNAs
- FMM 2 – Learn Motifs from Unaligned Sequences
- PITA 6 – microRNA prediction tool
- Nucleosomes Positioning 3.0 – Prediction by Genomic Sequence
- Genomica 3.040710 – Analysis and Visualization Tool for Genomic data
- GeneProgram 0.1 – Discovery of Functional Generality of Gene Expression programs
- JBD – Detect Binding Sites based on ChIP-chip data and Guides
- GRAM 0.6 – Discovery of Gene Modules and Regulatory Networks
- GSE – Database System for the Representation, Retrieval, and Analysis of Microarray data
- GPS 1.1 – Study Protein-DNA Interaction using ChIP-Seq data
- HTSeq 0.5.3 – Process and Analyze data from High-throughput Sequencing (HTS) Assays
- MochiView 1.45 – Genomic Sequences Browser
- SeqSaw 1.0.8 – Short Spliced Sequence Mapping Tool
- LookSeq – Alignment Visualization, Browsing and Analysis of Genome Sequence data
- ClustEx 0.31 – Responsive Gene Module Identification package
- CFinder 2.0.5 – Cluster data represented by Large Graphs
- Xid 1.1.2.41 – Design of Biological Experiments as a First Application Exploiting XEML
- Rast2Systrip 1.0.4 – Reconstruct and View Metabolic Networks
- Metaboflux 2.0.6 – Predict Flux Distribution in Metabolic Networks
- MIMTool 1.0.2 – Molecular Interaction Map drawing Tool
- PathVisio-MIM 2.0.11 – Pathvisio Plugin which Adds the Ability to Draw MIM Glyph
- HilbertVis 2.14 – Visualization of Genomic data with the Hilbert curve
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