Bioinformatics Toolbox Getting Started What Is the Bioinformatics Toolbox? Expected User Installation Required Software Additional Software Features and Functions Data Formats and Databases Sequence Alignments Sequence Utilities and Statistics Protein Property Analysis Phylogenetic Analysis Microarray Data Analysis Mass Spectrometry Data Analysis Graph Visualization Methods Statistical Learning and Visualization Prototype and Development Environment Data Visualization Algorithm Sharing and Application Deployment Examples Sequence Analysis Example: Sequence Statistics Determining Nucleotide Content Getting Sequence Information into MATLAB Determining Nucleotide Composition Determining Codon Composition Open Reading Frames Amino Acid Conversion and Composition Example: Sequence Alignment Finding a Model Organism to Study Getting Sequence Information from a Public Database Searching a Public Database for Related Genes Locating Protein Coding Sequences Comparing Amino Acid Sequences Microarray Analysis Example: Visualizing Microarray Data Overview of the Mouse Example Exploring the Microarray Data Set Spatial Images of Microarray Data Statistics of the Microarrays Scatter Plots of Microarray Data Example: Analyzing Gene Expression Profiles Overview of the Yeast Example Exploring the Data Set Filtering Genes Clustering Genes Principal Component Analysis Phylogenetic Analysis Example: Building a Phylogenetic Tree Overview for the Primate Example Searching NCBI for Phylogenetic Data Creating a Phylogenetic Tree for Five Species Creating a Phylogenetic Tree for Twelve Species Exploring the Phylogenetic Tree Phylogenetic Tree Tool Reference Opening the Phytreetool GUI File Menu Tools Menu Windows Menu Help Menu Functions - Categorical List Data Formats and Databases Sequence Conversion Sequence Statistics Sequence Utilities Pairwise Sequence Alignment Statistical Learning Protein Analysis Trace Tools Profile Hidden Markov Models Microarray File Formats Microarray Visualization Microarray Normalization and Filtering Microarray Utility Functions Mass Spectrometry Preprocessing and Visualization Scoring Matrices Phylogenetic Tree Tools Phylogenetic Tree Methods Graph Visualization Methods Tutorials, Demos, and Examples Functions - Alphabetical List Release Notes Bioinformatics Toolbox 2.0.1 Release Notes New Features Updated RBASE table Expanded Bioperl Demo Major Bug Fixes Zoom mode in msviewer is persistent New Tutorial Demonstrations Known Software and Documentation Problems Enable Java Figures on Macintosh Possible Perl error message with bioperldemo Warning message with Bioperl 1.4 Bioinformatics Toolbox 2.0 Release Notes New Features Mass Spectrometry Data Graph Visualization Statistical Learning Sequence Analysis Protein Analysis Microarray Analysis Enhanced Features Web Connectivity Sequence Analysis Microarray Data Analysis New Tutorial Demonstrations Known Software Problems Possible Perl error message with bioperldemo Warning message with Bioperl 1.4 Bioinformatics Toolbox 1.1.1 Release Notes New Features Major Bug Fixes Change to the data structure returned by affyread for CDF files. Changes to aminolookup.m varargin Possible Perl error message with Bioperldemo. hmmalign changes to match HMMER scores Bioinformatics Toolbox 1.1 Release Notes New Features Phylogenetic Analysis Functions Phylogenetic Tree Object and Methods Hidden Markov Model (HMM) Profiles aminolookup, baselookup blastncbi, blastread, getblast clustergram imageneread mapcaplot isoelectric seqdisp seqdotplot seqmatch New Demos Major Bug Fixes Corrected Emission Probability Platform Limitations for HP and IBM HP-UX Help Browser Limitations Bioinformatics Toolbox 1.0 Release Notes Introduction Features Data I/O Sequence Alignment Sequence Utilities and Statistics Microarray Normalization and Visualization Protein Structure Analysis Tutorial Demonstrations Printable Documentation (PDF) Product Page (Web)