Introduction | Performance Considerations | Preparing the Input Data | Choosing a Method and Model of Evolution | Building Minimum Evolution Phylogenetic Trees | Building Maximum Likelihood Phylogenetic Trees | Building Maximum Parsimony Phylogenetic Trees | Bootstrap and Jackknife Branch Supports | More Examples of Manipulating Dendrograms | Inspecting the Inputs and Outputs | Exporting the Tree | Generating a Summary Tree | Conclusion | Session Information

Introduction | Chimera Finding Problems | Getting Started | Obtaining/Building A Reference Database | Steps to Find Chimeras | Session Information

Introduction | Alignment Speed | Alignment Accuracy | Recommendations for optimal performance | Single Gene Alignment | Advanced Options & Features | Aligning Homologous Regions of Multiple Genomes | Session Information

About DECIPHER | Design Philosophy | Installation | Getting help | Functionality

Introduction | Getting Started | Inferring Demography | Inferring Recombination | Inferring Selection | Session Information

Introduction | Getting Started | Searching for hits between pattern and subject sequences | Aligning the search hits between pattern and subject | Controlling for false discoveries | Maximizing search sensitivity to find distant hits | Mapping long reads to a genome | Recommended search settings | Session Information

Introduction | Getting Started | Training the Classifier | Classifying Sequences | Creating a ``taxid'' file | Annotating Protein Sequences | Session Information

Introduction | The Objective of FISH Probe Design | Getting Started | Probe Design Steps | Dual Probe Design Steps | Session Information

Introduction | The Objective of Primer Design | Getting Started | Primer Design Steps | Additional Primer Analysis | Session Information

Introduction | Getting Started | Array Design and Validation Steps | Session Information

Introduction | Getting Started | Taking a first look at Obscurin | Detecting repeats automatically with DetectRepeats | Inferring the History of Repeats in Obscurin | Session Information

Introduction to supersized clustering | Getting started with Clusterize | Optimize your inputs to Clusterize | Visualize the output of Clusterize | Specialize clustering for your goals | Resize to fit within less memory | Clustering both nucleotide strands | Alternative measures of distance | Finalize your use of Clusterize

Introduction | Getting Started | Designing primers with diverse signatures | Assessing the Results | Session Information

Introduction | Getting Started | Building a Non-Coding RNA Model | Finding Non-Coding RNAs | Session Information

Introduction | Getting Started | Finding Genes in a Genome | Analyzing the Output | Incorporating non-coding RNAs | Annotating the protein coding genes | Guaranteeing repeatability | Exporting the output | Session Information