Mesquite Features

Below is a brief outline of Mesquite features. Many of the links within the outline take you to screenshots. To see features recently added to Mesquite, see the manual page on new features.

• Overview
• Analyses
• Characters
• Taxa
• Trees
• Other features

Overview

Primary entities are taxa (which may represent species, genes, samples, and so on), characters (features or variables), and trees.

• Files may contain:
  • Multiple matrices
  • Multiple taxa blocks
  • Multiple blocks of trees
• Files may be linked into projects
• Multiple files may be open simultaneously

Analyses

• Ancestral state reconstruction — manual page
  • Methods
    • Parsimony
      • Categorical & sequence data
        • Unordered
        • Ordered
        • Stepmatrices
      • Continuous data
        • Linear
        • Squared change (least squares)
    • Likelihood
      • Mk1 (one parameter) model for categorical data
      • Asymmetrical (2 parameter) model for categorical data
  • Display modes
    • Trace single character
    • Summary of all characters
    • Summary of a character's reconstruction over a series of trees
• Processes of Character Evolution — manual page
• Estimating parameters of categorical characters
  • Estimate rate in one-parameter Mk1 model
  • Estimate bias of rates of gain versus loss in 2-parameter model
• Comparative method/character correlation
  • Mirror Tree and Plot Tree visualizations
  • Pairwise comparisons for categorical data
  • Felsenstein's contrasts for continuous data (with PDAP package)
• Population Genetics & phylogeography — manual page
  • Gene trees can be embedded within population histories or species trees
    • Fit can be displayed graphically
    • Deep coalescences and Slatkin & Maddison's s assess fit of gene tree into species tree
• Coalescence simulations of gene trees within population histories to derive statistical expectations
• Population histories can include changes in population size, divergences, time
• Simulations and Randomizations — manual page
  • Parametric bootstrapping to test monophyly, explore long branch attraction, and so on
  • "Batch Architect" constructs repetitive analyses communicating with programs such as PAUP
  • See under Characters and Trees for discussion of simulation and randomization options
• Continuous valued characters
  • Mapping tree into 2D or 3D space
  • Simulations and ancestral state reconstructions
  • Multivariate analyses
    • Principle Components Analysis
    • Canonical Variates Analysis
    • Among-group PCA
    • Within-group PCA
    • Evolutionary PCA (similar to PCA but tree-based)
  • Geometric morphometrics
    • Reconstruction of ancestral landmarks
• Tree comparison
  • Tree similarity/dissimilarity indices
    • Shared partitions
    • Patristic distance correlation
    • Robinson-Foulds metric, unweighted or weighted (in TSV)
  • Host/parasite, gene/species and other contained/containing trees can be compared by deep coalescences, Slatkin and Maddison's s
  • Visualizations of tree space (with TSV)
  • Instability of terminal taxa among trees
• Tree reconstruction
  • Tree search
    • Any statistic for tree can be basis of search including treelength and fit of gene trees into species trees
    • SPR, NNI search with single as-is sequence (slow compared to PAUP & NONA)
  • Cluster analysis
    • Distances
      • Uncorrected distances
      • Distances among contained taxa (e.g., for species trees based on distances among contained genes)
    • Algorithms yield multiple trees in case of ties
      • UPGMA
      • Single Linkage
  • Creation of MRP (Matrix Representation with Parsimony) matrices from trees for use in constructing supertrees
• Other statistics: see under Characters and Tree
• Charts for character, taxa, trees and nodes summarize calculations results
• Bars and points can be colored to show the category of the objects
• Scatterplot points can be colored for third dimension
• Scatterplot can be used to show statistics in the context of protein structure

Characters

• Multiple matrices in each file
• Formats supported
  • Categorical characters
    • up to 56 states
  • DNA sequences
  • Protein sequences
  • Continuous valued characters
    • multiple items in each matrix cell
• Characters used in calculations can come from:
  • Matrices stored in files & edited by user
  • Simulationsof character evolution on a current tree
    • Simulated DNA sequence evolution
      • Subsitution models
        • Jukes Cantor
        • Transition/transversion bias (HKY85)
        • General Time Reversible
      • Base frequencies
        • Equal
        • Empirical
        • Specified
      • Rate variation
        • None
        • Gamma, with or without proportion invariant
        • By codon positions
    • Simulated Categorical character evolution
      • Mk1 model (one parameter, symmetrical gain/loss)
      • Asymm Mk Model (two parameters, bias in gain versus loss)
    • Simulated Continuous character evolution
      • Brownian motion model
  • Randomizations and other transformations of matrices
    • Bootstrap resampling
    • Reshuffling states among taxa
    • Rarefaction by characters (randomly deleting characters)
    • Rarefaction by cells (randomly changing cells to missing data)
• Spreadsheet data editor for character matrices
  • Edit character states
  • Add, delete characters
  • Search for cell contents or footnotes
  • Simple Footnotes to characters, taxa, cells of the matrix, character states
  • Multiple Annotations (including comments, images, references) can be attached to each character, taxon, and cell of matrix
  • Characters can be sorted by many criteria
  • Character selection
    • selection in one context (e.g. a data editor) is respected in others (e.g., a scatterplot)
    • magic wand to select characters by similar names or properties
    • select characters with probability p
    • select n characters randomly
    • select variable characters
    • select characters by partition
  • BLAST search for selected sequence
  • Display options
    • Color cells or text in cells by
      • state (e.g., different colors for ACGT)
      • value of a statistic (e.g., amino acid hydrophobicity; moving window of AT bias)
      • whether footnote is present
      • colors assigned by user
    • Character state names with categorical data
  • Transformations & editing
    • Categorical
      • Fill (paint bucket)
      • Random fill
      • Recode
      • Reverse sequence
    • DNA/Protein sequence
      • Nucleotide complement
    • Continuous
      • Fill (paint bucket)
      • Standardize
      • Random fill (with mean and variance)
      • Add random noise
      • Log transform
      • Add constant; multiply constant
  • Utilities to:
    • Concatenate matrices
    • Compare matrices
• Auxiliary information stored with characters
  • weights
  • parsimony model (unordered, ordered, etc.)
  • probability model (Mk1, Jukes Cantor, etc.)
  • inclusion/exclusion
  • partitions
• Statistics for characters
  • Can be viewed in bar charts, scattergrams and list window
  • Options include:
    • Values with trees
      • likelihood
      • parsimony steps
      • Likelihood-estimated parameters of character evolution
      Percent missing (unassigned)
    • Percent gaps (inapplicable)
    • Percent polymorphic
    • Amino acid size and hydrophobicity
    • Compositional bias (GC/AT bias)

Taxa

• Multiple taxa blocks allowed
  • Taxa blocks can be associated (e.g., genes in species)
• Selection
  • Selection in one context (e.g. a data editor) is respected in others (e.g., a scatterplot)
  • Magic wand to select taxa by similar names or properties
• Statistics for taxa
  • Can be viewed in bar charts, scattergrams and list window
  • Options include:
    • Continuous character state
    • Percent missing data
    • Compositional Bias (AT/GC bias)
    • Instability of taxon's relationships among trees

Trees

• Trees used in calculations can come from:
  • Trees stored in files and/or edited by users
  • Simulations of speciation or population genetics
    • Equal rates Markovian speciation
    • Equal rate speciation with subsequent sampling
    • Equiprobable trees
    • Coalescence simulations
    • Coalescence simulations within divergent population history
  • Randomizations of trees
    • Randomly augmented tree (taxa added, useful to explore value of further sampling)
    • Randomly rarefied tree
    • Reshuffled terminals
    • Randomly resolve polytomies
    • Add random noise to branch lengths
    • Randomly rearrange some branches
  • Exhaustive enumerations
    • All rerootings of given tree
    • All SPR or NNI rearrangements of given tree
  • Consensus trees
    • Strict (with TSV)
  • Transformations of trees coming from other sources
  • Filtered trees coming from other sources
    • Trees containing given clade
    • Trees having a given value (e.g. symmetry, treelength, etc.) greater or less than number specified
• Tree properties
  • branch lengths
  • branch widths (e.g. effective population sizes)
  • footnotes and names can be assigned to branches
  • hyperlinks to branches
  • internal unbranched nodes allowed
  • other properties can be added (branch color, etc.)
• Tree manipulation
  • Tools in tree window to:
    • Move branches
    • Collapse to polytomy
    • Reroot
    • Cut clade
    • Insert unbranched nodes
  • Reroot using outgroup
  • Adjust branch lengths
    • Interactive adjustment
    • Menu items to assign or scale branch lengths
    • Ultrametricize
  • Selection of branches
    • Indivdually
    • Select all in clade
  • Concatenate or extract tree blocks
• Tree viewing
  • Windows
    • Tree Window: interactive browsing and editing of trees
    • Multi Tree window: simultaneous viewing of several trees
    • Mirror Tree window: same tree viewed in mirror image to compare two analyses
    • Dependent tree window: an extra view of tree in Tree Window
  • display results of analyses (e.g., ancestral state reconstruction)
  • can show stored or live-simulated trees
• Tree display
  • Tree shapes
    • Diagonal branches
    • Square branches
    • Balls & Sticks (allows pie diagrams at nodes for likelihood)
    • Curvogram
    • Circular tree
    • Plotting tree in 2D or 3D space
  • Can vary colors, fonts, sizes, orientation
• Statistics for trees
  • Can be viewed in bar charts, scattergrams, list window and Tree Window
  • Options include:
    • treelength (parsimony)
    • asymmetry of tree
    • similarity with other tree or trees
    • fit of gene tree with species tree
    • correlation between two characters
    • estimated parameters of character evolution under tree

Other features

• Windows have both a graphics and a text view; text view gives detailed results of calculations
• Scripting language with loops and variables
• List windows allow management of taxa, characters, trees, and other objects
  • select objects
  • delete objects
  • set properties of objects (e.g., assign weights to characters)
  • view statistics of objects
• File formats
  • NEXUS is native format
  • Import/export of other file formats
    • NONA/Hennig86 (.ss)
    • NBRF
    • FASTA
    • CLUSTAL
    • PHYLIP
    • POY
    • Simple tables
    • Pagel (Multistate/Discrete)
• Auto-documentation
  • Web pages composed automatically to indicate use of tools and menus
  • Explanations of options embedded in choice dialogs
• Constructing tutorials and lab exercises
  • Navigator for tutorials and examples
  • Notes window
  • Image window
  • Can add links to web pages in navigator, tree window