2012 May
- JavaCycO – Java Library for connecting to BioCyc Pathway Geneome Databases (PGDBs).
- QuantProReloaded 1.0 – Software for the Statistical Analysis of Microspot Immunoassays
- LineUp – Statistical Detection of Chromosomal Homology
- CloseUp – Detect Chromosomal Homology Using Gene Density Alone
- Cyber-T – Software and Server for Analysis of DNA Microarray data
- GO-SCAN 2.2 – Gene Ontology for Significant Collection of Annotations
- MSCLtoolbox 200902 – Statistical Analysis of Microarray data
- P-SCAN 1.2 – Peak quantification using Statistical Comparative ANalysis
- F-SCAN 1.3 – Fluorescently Probed cDNA Microarray Analysis
- PSIPRED 3.3 – Accurate Protein Secondary Structure Prediction
- Twease 20090512 – Web-based tool to Search Medline
- BDVAL 1.2 – Biomarker Discovery in High-throughput datasets
- Annotare 1.3 – Tool for Annotating High-throughput Biomedical Investigations and Resulting data
- CryoBayes beta – Bayesian method for Inferring 3D structure of Macromolecules
- TFBS 0.5.0 – Perl modules for Transcription Factor Binding Site Detection and Analysis
- RRE 20040401 – Retrieval of Non-coding Regulative Elements from Annotated Genomic databases
- CLUTO 2.1.2a / gCLUTO 1.0 – Software for Clustering High-Dimensional Datasets
- PAM 2.1 – Prediction and Survival Analysis for Genomic Expression Data Mining
- COGRIM – Clustering of Genes into Regulons using Integrated Modeling
- STAC 1.2 – Significance Testing for Aberrant Copy-Number
- GSIM – Microarray Gene Expression Simulator
- PaGE 5.1.6 – Patterns from Gene Expression
- RUM 1.11 – Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper
- tpWY – t-statistics, p-values, and Westfall and Young step-down method
- mpMap 1.5 – Genetic Analysis of Multi-parent Recombinant Inbred Lines
- Spot 3.2 – Analysis of Microarray Images
- AffyExtensions 0.8-2 – Analyze Affymetrix data
- RMAExpress 1.0.5 – Generate RMA Expression Measures for Affy data
- SMA 0.5.13 – Statistics for Microarray Analysis
- SlideMap 1.2.1 – Create a Row/Column to Plate/Well Map of a Microarray Slide
- ExpressConverter 2.1 – Microarray Data Files Transformation Tool
- PLAN 1.0 RC19 – High-throughput BLAST Searches and Managing and Mining Results
- MSFACTs 1.0.1.3 – Metabolomics Spectral Formatting, Alignment and Conversion Tools
- MET-IDEA 2.08 – Data Extraction Tool for Mass Spectrometry-based Metabolomics
- MOLA – System for Virtual Screening using AutoDock4/Vina on Computer Clusters
- ArrayOme 1.0 – Estimate the sizes of Microarray-visualised Bacterial Genomes
- tRNAcc 1.0 – Identify Genomic Islands Associated with tRNA Genes
- GRIL 1.0.0 – Genome Inversion and Rearrangement Locator
- ASAP 1.4.1 – A Systematic Annotation Package for Community Analysis of Genomes
- Barphlye – Bayesian Analysis of Rearrangement Phylogeny in Yersinia
- GPODE – Learning Gene Regulatory Networks from Gene Expression Measurements
- ProbTF – Transcription Factor Binding Prediction from multiple data sources
- MultiTF-PPI – Competitive Transcription Factor Binding Prediction
- DSection – Probabilistic Analysis of Gene Expression Measurements from Heterogeneous Tissues
- Vim Alignment highlighting – Vim highlighting files for DNA sequence alignments
- Vim Nexus syntax highlighting – Nexus syntax highlighting files for the Vim editor
- Pensim 2.0 – Modularized Simulator for Penicillin Fermentation
- MIMAR 20101217 – MCMC Estimation of the Isolation-Migration model Allowing for Recombination
- codonbias 20060818 – Estimate Selection Coefficients relating to optimal Codon usage
- trueFS – Find Ascertainment Corrected Frequency Spectrum based on Ascertained SNP data
- PATRI – Paternity Analysis of Genetic Data
- MISAT 1.0 – Microsatellite Analysis by Maximum Likelihood
- SweepFinder 20060814 – Detect the Location of a selective Sweep based on SNP data
- Structurama – Infer Population Structure from Genetic Data
- Ginkgo 3.9.0 – Phylogeographical Evolution Simulator
- NCL 2.1.18 – NEXUS C++ Class Library
- Phycas 1.2.0 – Phylogenetic Analyses
- PhyloGeoRef – Java Library for Mapping Phylogenetic Trees and Geographical Information in KML
- trimAl 1.4 – Tool for Automated Alignment Trimming
- ETE 2.1 – Python Environment for Phylogenetic Tree Exploration
- Landmark 3.6 – 3D Morphological Models on Trees
- WOOF – Word-oriented Objective Function for Validation of Sequence Alignments
- STAMP 2.0.0 – Analyze Metagenomic Profiles
- RITA 1.0.1 – Rapid Identification of Taxonomic Assignments for Metagenomic fragments
- Radié 1.01 – Character Visualization and Computation Using Radial Phylogenetic Trees
- PICA 1.0.1 – Genotype-phenotype data Mining software
- NetworkDiversity 1.0.0 – Calculation of beta diversity over Phylogenetic Networks
- GANN 2.0 – Machine Learning tool for the Detection of Conserved Features in DNA
- EvolSimulator 2.1.0 – Simulation Test Bed for Hypotheses of Genome Evolution
- EEEP 1.01 – Efficient Evaluation of Edit Paths
- GeoPhyloBuilder 1.2.1 – ArcGIS Extension that Creates Geophylogenies
- HyperTree 1.2.2 – Java Phylogenetic Tree Viewer
- PhyloWidget – View, Edit, and Publish Phylogenetic Trees
- GARLI 2.0 – Phylogenetic Analysis of Molecular Sequence data using the Maximum-likelihood Criterion
- PhiSpy 2.2 – Find Prophages in Microbial Genomes
- PhiSiGns 1.2 – Indentify Signature Genes in Phages and Design Primers
- RTMg – Real Time Metagenomics
- riboPicker 0.4.3 – Identification and Removal of rRNA-like Sequences.
- TagCleaner 0.12 – Detect and Remove Tag Sequences from Metagenomic datasets
- FastQC 0.10.1 – Quality Control Tool for High Throughput Sequence Data
- Scripture Beta2 – Transcriptome Reconstruction
- PHLAWD v1 – Phylogenetic Dataset Construction
- T-REKS – Identification of Tandem Repeats
- STAR – Search for Tandem Approximate Repeats
- SDM – Fast Distance-based Approach for (Super)Tree Building in Phylogenomics
- QOD 1.0.2 – Alternative Approach to Multiple Genome Comparison
- PhySIC_IST – Cleaning Source Trees to infer more Informative Supertrees
- PhyD* – Fast NJ-like algorithms to deal with incomplete Distance Matrices
- MS_Align 2.0 – Comparison of Minisatellites
- SearchRepeats – Detection of Exact Repeats by a Compression Algorithm
- TD 2.0 – Computation of the Transformation Distance for a set of DNA sequences
- 2ZIP – Prediction of Leucine Zipper Domain from the Protein Sequence
- MPscan – Index free Mapping of multiple short reads on a Genome
- DTdraw – Tandem Duplication History Drawing Program
- DTscore – Fast and Accurate Distance Algorithm to Reconstruct Tandem Duplication Trees
- BIONJ – Distance based Phylogeny Reconstruction Algorithm
- DupTree – Large Scale Gene Tree Parsimony Analysis
- iGTP 1.1 – Infer Species Phylogenies from Gene Phylogenies
- CCOptimF – R code for fitting Random Periods Model
- PSPE – Simulate Evolution of Non-coding DNA Sequences
- OMiMa – Identify Functional Motifs in DNA or Protein Sequences
- ACANA – Accurate and Consistent Alignment Tool for DNA sequences
- MetISIS 1.0 – Metabolite In Silico Identification Software
- PointCloudXplore 2.0 – Visualization and analysis of the data in PointCloud and Virtual Embryo Files
- TiMAT 3.4.4 – Process Chip-chip Tiling Array Experiments
- FARMS 1.4.1 – Factor Analysis for Robust Microarray Summarization
- jLSTM / LSTM – “Long Short-Term Memory” for Protein Classification
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