MacClade 4.02: Who Says Data Doesn’t Grow on Trees?
MacClade is a useful program for those who wish to demonstrate systematic and evolutionary ideas in the classroom or want an editor for manipulating trees and data matrices. MacClade allows users to examine data in a phylogenetic perspective. Available for computers using the Macintosh operating systems, it also can be run, with some limitations, under MacOS emulators.
Data Editing and Analysis
MacClade is an excellent editorial tool—I regularly use it to teach my molecular phylogenetics class, and the first thing we do is use it to organize data downloaded from the Web. Genetic data is easily loaded and formatted into MacClade from the various data formats available from such public databases as Entrez (the national gene repository). The software can support many standard formats such as Genbank, Fasta, and NBRF, as well as standard alignment formats such as clustalx for users who wish to align the sequences prior to loading the data. These data input features are handy for formatting in preparation for phylogenetic analysis. Users can also enter characters and states of morphological or behavioral data by hand. The program not only supports discrete character state data, but also handles polymorphic characters as well as continuously varying ones.
MacClade allows users to edit data and examine the characters on a tree, but strictly speaking, it should not be used to conduct a phylogenetic analysis. It is better to use specific phylogenetic software with the search algorithms necessary to ensure a rigorous tree search. When building trees in MacClade's tree window, users are doing a kind of limited tree search, but for larger data sets this software should not substitute for a serious analysis. The product is best used in collaboration with software designed for this purpose such as Mega, Nona, Paup4, TNT, and Winclada. MacClade's friendly user interface and pull-down menus allow import of numerous formats, including results from most phylogenetic software.
Teaching with MacClade
MacClade is an excellent teaching tool for systematics and evolution. Students can determine the characters and states from their own observations, or they can download comparative molecular data and load it into the data editor for analysis. For four taxa there are only three possible trees, and in the MacClade tree window one could look at all possible trees to see which of these best explains the data. As the number of taxa increases, however, the number of possible networks and trees d'es as well, and this is why for larger problems one should complement MacClade with phylogenetic software.
Numerous features in the data editor allow investigators to weight the data, include or exclude it, designate outgroups, pick the coding frame, translate sequences to proteins (virtually), decide treatment of gaps and missing data, and much more. Included sample files give beginners a head start on getting the proper formats for the different sorts of data and treatments of data. Particularly valuable to both experts and novices in systematics is a set of tools devoted to manipulating trees and describing their character information. Trees can be edited by changing the tree root, moving branches around, collapsing branches, removing taxa, or pruning an entire clade.
Many important concepts of systematics can be demonstrated to students with this software. For example, trees with equal weighting have the same tree length for the same network, regardless of where the tree is rooted for the same network. Students can learn this important lesson about trees by selecting the root of the tree and watching the tree length remain unchanged. They can also look at different networks by moving taxa and branches around while maintaining the same root. In this way they can see the tree length change and thus determine which is the best explanation of their data. Understanding the difference between rooted and unrooted networks and how this affects tree lengths is a fundamental aspect of systematics that is often misunderstood by students.
Another important set of tools in the tree window optimizes characters on a tree. Investigators can see the evolutionary pattern of characters and toggle through them to see the evolutionary optimization for the states of each. This is a valuable tool for interpreting convergence among characters (independent gains or reversals of character change). The program will also list the detailed tree statistics, and trees can be saved to pict files and/or printed.
The Forest for the Trees
MacClade has some limitations, but this is largely in the realm of expert users. For example, genetic alignments with thousands of taxa in them will generate an error message of "too many taxa in the data matrix." This d'es not seem to be a problem associated with Macintosh memory, but a limit to the size of the data matrix the program can hold. Most users and classroom applications will not encounter these problems, however, so I highly recommend the program.