Mesquite Manual Table of Contents

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Part I: Mesquite Basics

• Introduction
• Learning how to Use Mesquite
• Why Mesquite was made
  • Overview
  • Practical Answer
  • Poetic Answer
  • Mesquite versus MacClade
• How Mesquite works
  • Overview
  • The tree of modules
  • Duties
  • Flexibility
• Installation
  • Mac OS X
  • Mac OS 9
  • Linux/Unix
  • Windows
• Basic concepts and vocabulary
  • Taxa
  • Characters
  • Trees
• Files
  • Making, opening, and saving data files
  • Projects
  • Opening versus including versus linking files
• Menus
  • Overview
  • Learning about menus
  • Standard menu items
    • File
    • Edit
    • Characters
    • Taxa & Trees
    • Analysis
    • Window
    • Help
  • Where to find menu items
• Mesquite's Windows
  • Overview
  • Common features of windows
    • Overview
    • Information bar
    • Mini scrolls
    • Tool palettes
    • Annotation area
    • Explanation area
    • List windows
• Charts
  • Overview
  • Selection of objects in charts
  • Auto-recalculation
  • Bar & Line Charts
    • Overview
    • Example: Robustness of estimated bias in character evolution
    • Example: Compositional bias along a sequence
    • Calculating and formatting options
  • Scattergrams
    • Overview
    • Example: Canonical Variates Analysis
    • Example: Correlation between variability and hydrophobicity
    • Calculating and formatting options
• Scripting and Macros
  • Overview
  • Macros
  • Learning about scripting
  • Commands within scripts
  • Scripts
  • Variables: Integers, Strings, and Objects
    • Overview
    • Numerical variables
    • String variables
    • Object variables
    • The variable "It"
  • Flow and command control
  • Debugging and technical details
• Modules
  • Managing Modules
  • Installed versus loaded versus running modules
  • Where modules are installed
  • Modules currently in use
  • Information pages and Manuals for modules

Part II: Characters, Taxa, and Trees

• Characters
  • Overview
  • Creating a character matrix
  • Deleting and renaming character matrices
  • The Character Matrix Editor
    • Overview
    • Adding, deleting, renaming, and sorting taxa and characters
    • Entering character data
    • Selecting taxa, characters and cells of the matrix
    • Copy/paste
    • Editing Names of Characters and States
    • Annotations
    • Coloring cells of the matrix
    • Alterations and Transformations
  • Changing the attributes of characters
  • Charting information about Characters
• Taxa
  • Overview
  • Creating and managing taxa blocks
  • Managing taxa
  • Renaming taxa
  • Assigning group membership
  • Associating two taxa blocks
• Trees
  • Overview
  • Characteristics of trees
  • Analyzing trees
    • Overview
    • Tree to tree similarity measures
    • Consensus trees
    • Fits of trees into trees
    • Taxon instability among trees
  • Stored trees and tree blocks
  • Tree sources
  • Filtering trees
  • Modifying trees automatically
  • Editing trees
    • The Basic Tree Window
    • Tree source
    • Moving from Tree to Tree
    • Storing trees
    • Tools
    • Alter/Transform menu items
    • Analyses
  • How trees are drawn
  • Printing trees and saving graphics files
  • Dependent Tree Window
  • Mirror Tree Window
  • Multi Tree Window

Part III: Analyses

• Character Evolution
  • Overview
  • Visualization of Character Evolution
    • Reconstruction of Ancestral States
      • Overview
      • Tracing the history of a character
      • Tracing all characters
      • Tracing character over multiple trees
    • Reconstruction Methods
      • Parsimony
        • Parimony models
        • Assigning a model
        • Creating & editing stepmatrices
      • Likelihood
        • Overview
        • Likelihood models
        • Making, editing, and applying probability models
        • Optimization settings
        • Reporting of results
      • Stochastic Character Mapping
    • Comparisons with other programs
      • NEXUS-based programs
      • MacClade
      • Pagel"s Discrete & Multistate
    • Acknowledgements
    • References
  • Analyses of Character Evolution
    • Processes of character evolution
    • Estimating parameters for single characters
    • Correlations among characters
      • Visualizations
        • Mirror tree window
        • Plot tree 2D
        • Plot tree 3D
        • Taxa scattergram
      • Pairwise comparisons
      • Felsenstein's Independent Contrasts
      • Pagel's Correlation Method
      • Use with Pagel's Discrete & Multistate
    • References
• Diversification
  • Simulating speciation and extinction
  • Lineages through time
  • Speciation and extinction rates
  • Character-dependent Speciation and extinction rates
• Simulations & Randomizations
  • Overview
  • Simulating and randomizing characters
    • Character Simulations and Randomizations for statistical tests
      • Overview
      • Using results of simuations & randomizations
      • Simulations of character evolution
      • Viewing results of simulations
      • Randomizing characters
    • Simulating DNA sequence Evolution, with examples of hypothesis testing
      • Overview
      • Simulating DNA sequence evolution on a tree
      • Building more complex models
      • Batch Architect: Simulating, exporting, and analyzing multiple matrices
      • Examples of tests of phylogenetic hypotheses
        • Example I: Testing monophyly of a group of beetles
        • Example II: Are strepsipterans related to flies?
    • Simulating coalescence and sequence evolution within populations
      • Introduction
      • Importing and Exporting Data
      • Single populations
        • Coalescence Simulations
        • Example: Chart of coalescence depths
      • Multiple populations or species
        • Analyzing gene trees for multiple populations or species
        • Establishing the association between genes and species/populations
        • Editing already-created taxa associations
        • Simulating coalescence within a species/population tree
        • Reconstructing gene history within a species/population tree
        • Visualizing gene history in a species/population tree
        • Measuring fit between genes and species/population trees
          • s of Slatkin & Maddison
          • Deep coalescences
          • Gene duplications/extinctions
          • Example: Effect of population divergence time on s
        • Inferring the population or species tree
          • Tree search
          • Cluster analysis
      • Simulating sampled gene sequences
        • Introduction
        • Generating a single matrix of sequences
        • Generating a series of matrices
        • Example: Multiple simulations of sequence samples
      • References
  • Simulating and randomizing trees, including species trees and gene trees
    • Introduction
    • Using results of simulations & randomizations
    • Evolutionary Simulations of Trees
      • Species Trees
      • Gene Trees
    • Random Trees
    • Randomized Trees
• Molecular Data
  • Introduction
  • Editing molecular data
  • Format
  • Alter/Transform Tools
  • Alignment
  • Finding sequences
  • Display of sequences
  • Managing molecular matrices
    • Overview
    • Include Taxa from File
    • Fused Matrix Export
    • Archiving Taxon Names
    • Translation to Protein
  • Interactions with GenBank
  • Simulating DNA sequence evolution
  • Statistics for DNA sequences
    • Overview
    • ACGT Compositional bias
    • Character Compositional bias
    • GC bias coloring of matrices
  • DNA Distances
  • Statistics for Protein sequences
    • Site hydrophobicity
    • Amino Acid hydrophobicity
  • Visualizing protein tertiary structure
  • Sequence Data within populations
  • Reconstructing ancestral states
• Continuous Data
  • Continuous characters overview
  • Editing continuous data
  • Reconstructing ancestral states
  • Plotting trees
  • Simulating character evolution
  • Ordinations
  • Tree reconstruction
  • Felsenstein's independent contrasts
  • Geometric morphometrics

Part IV: Miscellaneous Debris

• Interactions with other programs
  • Why?
  • Importing/exporting files
    • Overview
    • MacClade
    • PAUP
    • NDE
    • CLUSTAL
  • MrBayes interactions
  • CLUSTAL (broken link?)
• Publishing Results
  • Important information
  • How to cite Mesquite?
    • General
    • Analyses
    • What to cite
• Support & Advice
  • If you think you've found a bug...
  • Suggesting new features
  • Why is this bug here?
  • Help system
  • Reporting bugs & requesting advice
  • Mesquite Listserv
  • Java bugs that affect Mesquite
• Programming in Mesquite
  • Mesquite source code
  • Obtaining Mesquite source code
  • Using Eclipse for Mesquite development
    • Installing Eclipse
    • Installing Subclipse subversion plugin
    • Subversion checkout of Mesquite source
    • Creating a Mesquite launch configuration
  • Developing your own modules
  • Contributing changes to the official Mesquite code
  • Mesquite development mailing list
  • Developement Reference
• Help
  • Why Mesquite is complex
  • Documentation
  • How to remember or document what you've done
  • MesquiteFAQ
  • Programming in Mesquite
  • Two Examples:
    • Example I: Testing monophyly of a group of beetles
    • Example II: Are strepsipterans related to flies?
• Credits & Acknowledgments