List of Features

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

Overview

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

Files may contain:Files may be linked into projects
- Multiple matrices
- Multiple taxa blocks
- Multiple blocks of trees
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)
Processes of Diversification — manual page
- Simulations of birth/death process
- Lineage through time plots
- Likelihood inference of a character's effect on speciation/extinction rates
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 Trees
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 searches:
  - search for matches to selected region
  - import into matrix top BLAST matches
- Display options
  - Color cells or text in cells by
    - state (e.g., different colors for ACGT)
    - amino acid into which the codon would be translated
    - 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
    - Reverse complement
    - Alignment:
      - manual alignment tools allow you to move blocks of the sequence by hand
      - automated pairwise alignment tool
      - send selected block of matrix to Clustal, MAFFT, or Opal and incorporate the aligned result
  - 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
Distances
- Jukes-Cantor, Felsenstein 81, Kimura 2-Parameter, Felsenstein 84 distances
- Great Circle distances in the separately-released Cartographer package
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)
  - "Simple NEXUS" files for MrBayes
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

Mesquite's Features