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Highlights of some new features in MacClade 4

The new version of MacClade will have many improvements in user-interface, as well as much more extensive tools for data manipulation. This page highlights a few of the changes, concerning:

Editing data
Consensus sequences
List windows and the selection and manipulation of objects
Interactions with PAUP


Editing data


There are many changes in MacClade's data editor, including many new display modes and editing tools. Some of these are general, but the majority are designed for use with molecular sequence data. Here we will mention of few of these.

Display of data

There are many options for how data can be displayed. Here are two examples.

You can ask MacClade to color data cells so that the patterns of state variation are more evident:

With protein-coding nucleotide data, you can ask MacClade to show the amino acid translation. This translation is "live", in the sense that changes to the nucleotides, for example through use of the alignment tools (see next section), cause immediate updates to the amino acids shown.

Tools in the Editor

In MacClade 3, there is only one tool available in the editor: the arrow. MacClade 4 has a tool palette, with 17 tools:

Many of the tools have multiple functions and options; brief descriptions of some of their functions follow:



Standard tool: this is more or less the same as what is was in MacClade 3

Block selector: selects blocks in the matrix

Selection wand: In standard mode, if you touch on cell in the matrix, and it is a gap, then the largest contiguous piece of gaps containing that cell is selected, restricted to one taxon; if it is not a gap, then the largest continuous piece of non-gaps containing that cell is selected. If you touch on a taxon name, all taxon names are selected; if you touch on a character name, all character names are selected. There are other modes, with different behaviors.

Select to end tool: If you touch on cells in matrix, it will select from that cell to the end (or start, depending upon the mode) of the matrix.

Scissors tool: excises pieces of the matrix. It removes the data and moves the remainder of those sequences to the left (or right, depending upon the mode).

Stamp clipboard tool: Select a block of cells, and copy them to the clipboard. Then choose this tool, and you will be able to move the clipboard contents around the edtior. To paste the contents onto a region, click the mouse button to stamp the cells down.

Pairwise alignment tool: drag one sequence on to another, and a simple Needleman-Wunsch algorithm will be performed, aligning the dragged sequence onto the one on which it is dropped.

Block move tool: this is the main manual alignment tool. To use it touch on a nucleotide or amino acid; MacClade will automatically grab and let you move an entire chunk of the sequence (by an entire chunk, we mean the largest contiguous piece of non-gaps). You will be able to move it forward and backward through any bounding gaps. There are several options for this tool, which affect the mode of action.

Selected block tool: an alignment tool that lets you move selected blocks in the matrix. Equivalent, more or less, to the block move tool, except that it only works on selected blocks, and doesn't allow you to split a block. The advantage is that it allows you to move multiple sequences at once. Valuable in conjunction with the magic wand tool.

Close gaps tool: this tool moves the selected block as far to the left or right as possible, by shifting the block to close any adjacent gaps.

Split Block tool: allows you to split a block of data to introduce gaps; must be used on boundaries between cells.

Split others tool: Similar to the split block tool except that it moves all sequences OTHER than the one being dragged.

Eyedropper tool: touch on a cell in the matrix and MacClade will use the state in that cell as the paint state; touch on a taxon name or a taxon number and the paint state will be the state present in that taxon. e.g. say taxon 5's number is touched on, and the states for taxon 5 are 01102 for the first five characters. Then using the paintbrush or paintbucket on any taxon's character 1 will paint state 0, any taxon's character 2 will paint state 1, and so on.

Paint brush tool. use this tool to set the state of any cell touched on to be the state represented by the "paint" (see the eyedropper tool, above, for a description of the paint options and how one changes the paint).

Paint bucket tool: use this tool on a selected block of cells and that block will be filled with the state represented by the "paint" (see the eyedropper tool, above, for a description of the paint options and how one changes the paint) or with random data, depending upon the mode. You can also restrict the paint bucket so that it only fills cells containing a particular state. You can also specify the MacClade not fill every cell selected, but instead a chosen fraction. For example, if you choose 0.1 as the fraction, then MacClade will fill each of the chosen cells with a probability of 0.1; thus, on average, only 10% of the cells will be altered.

Pop-up states tool: touch this on a cell, and a menu will pop up listing the states for that character. Choose one, and that state will be entered into that cell. If the states have been given names, those state names will be displayed in the pop-up menu.

Show picture tool: touch this on a cell to which a picture has been attached and the picture will be displayed.


An example tool: Block Move

Several of the tools allow you to manual align sequences by moving all or part of them. For example, let's say you wanted to move the middle of these three sequences to the left. You could grab the sequence with the "block move" tool in the editor, and push the second sequence to the left:

As you are moving the sequence MacClade updates the amino acid translation:

When you have moved it to where you wish you can let go:


 This is one of the many tools with options that allow you to control the behavior of the tool. For example, with this tool

  • if Allow Matrix Edges to Expand is chosen, then MacClade will add more characters to the start or end of the matrix to make room for sequences pushed off the start or end.
  • if Move Entire Sequence is chosen, then the entire sequence, exclusive of terminal gaps, will be moved
  • if Accumulate Sticky Blocks is chosen, then as you move one piece along, if it bumps into another piece, then that other piece will be joined to the first piece and you will now be moving both pieces, as one.
  • if Allow Block Splitting is chosen, then the Block Move Tool behaves as the Split Block Tool when the mouse is over the boundary between two cells

An example tool: Scissors

The scissors tool excises pieces of the matrix.

For example, if one used it on following selected block:

those 12 cells would be removed from the matrix and the end of the six sequences would be shifted to the left:

An example tool: Split Others

When one clicks on the boundary between two characters in one taxon and pulls to the right or left, this tool moves all the OTHER taxa to the right or left. For example, if one positioned the tool as shown:

and pulled one column to the right, all other sequences would be moved to the right, and gaps inserted:


Consensus sequences

MacClade 4 can calculate and display consensus sequences. There are several options for the calculation, allowing one to display consensus sequences of varying stringency. In the figure below, two different consensus sequences are shown: 

You can choose to have the consensus sequences calculated over all taxa, or only over a particular set of taxa.


List windows and the selection and manipulation of objects

In MacClade 3, there is a Character Status Window which lists the characters and their various properties. This is the window in which you can change the weights and types of a character. In MacClade 4, the Character List Window has been much improved, and there are now also equivalent windows for taxa, trees, weight sets, type sets, inclusion sets, character sets, and taxon sets. In these windows you can rename, reorder, delete, and modify these objects.

In the list windows, there are three tools available:

The selection wand will select any similar object. For example, if you use it on any of the columns in a list window to the right of the name column, it will select all objects with the same value in that column. For example, if you touched on a "2" in the States column in the Character List window:

 then MacClade would select all objects that have two states:

With this you can select all taxa without missing data, or all trees with polytomies, or all characters of a particular weight, and so on. You can then edit them as appropriate.

Interactions with PAUP*

There are a number of features added to MacClade 4 to improve interactions between PAUP* and MacClade. Here are three examples:

Nexus block management

You can now manipulate various NEXUS blocks contained in the data file, including PAUP blocks. This allows one to edit commands that PAUP will process when it executes the file.

Constraint Trees

You can ask MacClade to save the tree on the screen as a constraint tree. If you do this, save the file in MacClade, and then re-execute it in PAUP*, the constraint will be available for use with PAUP's searching and filtering commands.

Decay Index

While MacClade 4 does not calculate decay indices (Bremer support values) itself, it will create a PAUP file containing the text commands necessary to calculate the decay index values of all clades on the tree in MacClade's tree window. If you then execute this file in PAUP, PAUP will perform all of the relevant searches to calculate decay indices.


Copyright © 2011 by David R. Maddison and Wayne P. Maddison.
 All rights reserved.