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MacClade 4: Analysis of Phylogeny and Character Evolution

David Maddison, University of Arizona and Wayne Maddison, University of British Columbia

Publication Date: 2000
ISBN: 0-87893-470-7
$125.00
CD-ROM

MacClade 4 Program Features

* new to Version 4

Data Editor

The data editor maintains an enhanced, easy-to-use spreadsheet for editing character data. Many of the tools and display options are designed specifically for nucleotide and amino acid data. Data cells can be colored in several ways, including by translated amino acid for protein-coding nucleotide data, using any of the 12 built-in genetic codes or a user-defined code. Multiple consensus sequences can be created, of varying stringencies. Among the numerous tools are a pairwise alignment tool for automatic alignment of two sequences, and various tools for moving and splitting portions of sequences.

Version 4 contains numerous tools for data manipulation in addition to those for sequence alignment, including the ability to sort taxa or characters, quickly select blocks of cells, fill blocks of cells with a designated state or to match that of a particular taxon.

• Edit data matrix using built-in spreadsheet with states indicated by symbols (e.g., 0 to 9, ACGT, amino acid codes) or by full state names (e.g., "blue")
• Cut, paste, move columns and rows of matrix
• *Many manual sequence alignment tools and an automated pairwise alignment tool
• Recode or search and replace states automatically, including complement and reverse for molecular sequence data
• *Sort taxa or characters by state or alphabetically; shuffle data randomly
• *Find sequences of molecular data
• *Color cells of matrix by several criteria, including amino acid to which a codon would be translated
• *Simultaneously see nucleotides and translated amino acids
• *Multiple consensus sequences of specified stringencies
• *12 predefined genetic codes, plus ability to define custom codes
• Store footnotes or pictures for each cell in matrix
• *Tools for quickly filling data cells
• Generate random data; *fill percentage of cells randomly with random data or specified states
• *"Pretty printing" of matrix

Integration with PAUP* and Other Programs

MacClade 4 uses the same NEXUS file format as PAUP* 4, and thus data files and tree files can be shared between the programs with ease. In addition, several new features designed to improve MacClade/PAUP* interactions have been added. The tree in MacClade's tree window can be converted into a constraint tree in a PAUP* block for use in PAUP*; outgroups can be designated within MacClade; PAUP* blocks and other NEXUS blocks can be edited directly in MacClade.

MacClade can produce a PAUP* command file that will allow automated calculation of the decay indices of the clades present in the tree in MacClade's tree window.

MacClade can also share data with other programs, as it can import files in the following formats: PHYLIP, HENNIG86, NONA, NBRF, Clustal, GCG/MSF, FASTA, GenBank, GenPept, and tab-delimited text. It can export files in PHYLIP, HENNIG86, NONA, NBRF, tab-delimited text, and MEGA formats.

List Windows

Objects in MacClade (characters, trees, taxa, taxon sets, among others) are organized for easy manipulation in list windows. This unified interface has powerful tools for editing the objects, including selecting or sorting of rows via any listed values.

• *Unified interface for manipulating objects and viewing their values
• *Wand for selecting all rows by column values
• *Manually and automatically sort rows of list
• Define character sets and *taxon sets for rapid selection and use in other programs

Manipulating Phylogenetic Trees

MacClade 4 includes the same tools for graphical manipulation of phylogenetic trees, including easy rearrangement of branches, rerooting of clades, and so on. Several of the tools have been enhanced. The tool that searches for most-parsimonious trees is much more powerful, and a new tool for searching for optimal ancestral assignments with stratigraphic data is included.

• Pick up and move branches on screen using the Macintosh's mouse
• Automatic NNI and *SPR restricted above or below a selected clade
• Reroot clade at selected branch, *reroot within clade
• Move observed taxon into ancestral position
• *Automatic searching for optimal assignment of ancestors when stratigraphic characters present
• Collapse branches to yield polytomous trees
• Undo last branch move
• Cut taxa from tree
• Generate random trees
• Store and retrieve trees from data file or external tree file
• *Selection wand for selecting all taxa in a clade

Analyzing Character Evolution

In addition to the same features present in Version 3 of MacClade, MacClade 4 now has a much enhanced Trace All Changes feature, in which much more detailed information is displayed about each reconstructed change. Symbols can be used to indicate how a particular character is changing elsewhere on the tree, and the color of the symbol can be a function of an index such as the retention index, or whether the change is a transversion or transition, or the codon position of the character.

• View most parsimonious reconstructions of character evolution shown by "painting" the branches with different shades

For discrete-valued characters:

• Fix state at branch to investigate alternative hypotheses of character evolution
• Use up to 26 character states
• Analyze morphological, behavioral, molecular, and other data, with special formats for DNA, RNA, and protein sequences
• Code the state of a taxon as monomorphic, missing, polymorphic, or of partially uncertain state
• Assume character state transformations to be unordered, ordered, irreversible, Dollo, or of user-defined type in which the user indicates by matrix or *character state tree how many steps it is from one state to another
• Use Fisher's stratigraphic parsimony
• Weight or exclude characters
• View a summary, over all characters, of character states or changes on each branch
• *Trace All Changes mode now indicates value of index (consistency, retention, etc.), or codon position, or nature of change (transition/transversion) for each character changing, as well as the nature of evolution in the character elsewhere on the tree
• *Temporarily trace character in Trace All Changes mode
• Display graphical overview of character distributions
• Statistically test for concentration of evolutionary changes

For continuous-valued characters:

• *Reconstruct character evolution using linear or squared-change parsimony

Statistics and Charts

MacClade's charts summarize reconstructed character evolution over multiple characters and multiple trees.

• Display number of steps, consistency and retention indices for each character and totals for all characters combined
• View charts comparing characters for their number of steps, changes, and so on, along sequence or by codon position for molecular data
• View charts comparing trees for their treelengths, steps in individual characters, and so on
• View charts summarizing frequency of reconstructed changes between states
• Charts can summarize results over single or multiple trees and single or multiple characters

Other features

Data matrices can be exported as web pages, with many of the display options available in the data editor also available on the web pages.

• Print publication-quality trees with many options including slanting taxon names and various fonts using Postscript laser printers

• *"Pretty printing" of data matrices
• *Export data matrices as web pages
• *Place text version of tree display in clipboard
• Maximum number of 1,500 taxa and 16,000 characters, but depends on memory
• *Classroom Version included, with restrictions on editing that can be set on a file-by-file basis by the teacher

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