1 PAUP tutorial - Macintosh The following tutorial is based on the tutorial provided with the PAUP package (but modified to emphasise morphological analysis, and updated to refer to the current command-line Mac version). It provides a very brief overview of the basic usage of PAUP* 4.0. This tutorial was designed for people with no prior experience using PAUP. If you are already familiar with PAUP* then you will probably wish to skip this tutorial. We assume that users are familiar with basic phylogenetic terminology and operating system specific issues. As you become more experienced using PAUP, you will discover that there are many alternative ways to execute the operations described below. For obvious reasons, we have chosen not to describe all the possibilities in this tutorial; however, we encourage you to explore other menu and command-line options as your time permits. Several versions of PAUP* 4.0 are currently available. These versions fall under three general interface types: Macintosh PowerPC (now obsolete), Windows, and Portable (including current Mac). The Macintosh PowerPC interfac allows you to execute commands via menus and the command-line, but this version will no longer run on any current mac. The Windows and Portable (DOS, Unix and current Mac) interfaces are almost entirely command-line driven. Some menu functions are available in the Windows interface; however, these functions mostly include file and edit operations. This tutorial will use command-line syntax of the mac version. While you will be entering commands separately (one at a time) during this tutorial, note that PAUP can run in batch mode (where multiple commands can be combined into a single text file and processed sequentially by executing that command file). Some batch file examples are at the end of this tutorial. In this tutorial, commands to be typed are in bold courier font. Paup is generally NOT case-sensitive, but other phylogenetic programs (notably BEAST) are. Beware. 2 1. EXAMINE THE DATA FILE Choose your favorite Plain Text editor (e.g., TextWrangler, Textedit) to open the sample file named squamates.nex Textwrangler is included in the tutorial folder but is also available here as a free download: www.barebones.com/products/textwrangler/ The data are morphological and molecular data for a range of lizards and snakes. In particular, many extinct marine lizards are included, in order to test their possible affinities to snakes. Scroll through the file. Note following: The datafile consists of a character-by-taxon matrix of discrete traits, with additional Nexus “stuff” before and after. Anything in square brackets [e.g. comments describing the Nexus format] are ignored by PAUP*. The is divided into blocks of text, delimited by the words "begin" and "end". The word following "begin" defines the block-type e.g. TAXON block. In this example, the following types of blocks are used: ASSUMPTIONS, SETS and PAUP. As an example, the SETS block defines sets of characters and taxa, which can then be readily excluded and included using simple PAUP commands. You can have several blocks of the same type, e.g. multiple PAUP blocks specifying different analyses, or multiple SETS blocks specifying different sets of taxa and/or chraracters. There are, however, numerous other Nexus block-types. One of the advantages of the Nexus format is that applications will simply skip over blocks that they do not recognize. For a more detailed discussion of the Nexus format see Maddison, et al. (1997). For this example, you will not need to modify the original sample file. Notice that spaces in taxon names must be replaced with an underscore character _. Also, PAUP* does not pay attention to the character case in taxa labels. To make a new PAUP datafile: You can enter new data matrices in Mesquite which will save the matrix as a nexus file readable by PAUP, see the Mesquite tutorial. Otherwise, you can use Excel or Word or similar program to generate a matrix. If using Excel or Word, export the Excel data as a space-delineated file; PAUP does not mind if there are spaces between characters in the matrix [but DOES require a space after the taxon name]: Mosasauria 1 0 1 0 and Mosasauria 1010 are both treated the same. After you export the bare matrix from Excel etc, you will then need to manually add the Nexus “stuff” before and after. 3 2. OPEN PAUP Create a new folder on your desktop (not in a subfolder) called Paup_Tutorial (using underscore_ and capitals as shown). Copy squamates.nex to this folder. For Mac, Paup operates via the Terminal interface – the command-line system that “hides” behind the icon-driven desktop you normally use. If you double-click the PAUP icon you will automatically open and run PAUP in this interface, However, you can also open this interface first and then run PAUP. Open the terminal application with comes with all macs (under Applications / Utilities / Terminal), drag-and-drop the PAUP program to the command line, and hit return. In the Terminal window where PAUP is running, make Paup_Tutorial your working folder by typing the following (cd means change directory): cd /Users/user/Desktop/Paup_Tutorial Hit return to submit the command. The above command can be case sensitive on some mac settings – so make sure your capitalization matches your folder. Alternatively, just type cd followed by a space, and then drag-and-drop the folder Paup_Tutorial to the command line – the path and folder name will appear automatically! 4 IMPORTANT: folder names along the entire path to your working folder cannot have a space in the folder name, e.g. a folder name called “my stuff” is not permitted, but “my_stuff” is OK. Unless told otherwise (by putting a different path before filenames), PAUP* will read and write to files in the working folder, currently set to /Users/user/Desktop/Paup_Tutorial To change the working folder at any time (e.g. if you want output to be written into a different folder), type cd followed by a space, then drag-and-drop the new working folder onto the command-line. PAUP will read and write to files in the new folder. 3. EXECUTE THE DATA FILE Type: EXECUTE squamates.nex;[hit return to submit command] Note: you can often abbreviate commands to the first three letters: EXE squamates.nex; If your paup file is not in your working folder, you can type EXECUTE followed by a space, and then drag-and-drop the PAUP file onto the command line. The path to the file will be auto-populated (e.g. /Users/user/Desktop/Some_Other_Folder/Some_Other_SubFolder /squamates.nex) PAUP should execute the file and give you a summary of the contents: 4. LOG RESULTS TO FILE Ordinarily, you will want to log the results of a PAUP* session to a disk file to have a record of the results of your analyses. To echo the screen output to a file, LOG start file=practice.log; By default, this log file will be created in your working folder (so it adds this path to the filename, ie /Users/user/Desktop/Paup_Tutorial/practice.log) and all screen output sent to it. Have a look and you should see this file appear. Again, you can 5 change the folder for this log file by changing your working folder (or by adding a different path to the filename). To stop logging at any time, Type log stop; 5. SUMMARISING THE DATA Now that the data matrix has been processed, you can use PAUP* to obtain basic summary information about the data set. To start, you will display information about the characters included in sample data set. cstatus; PAUP* will display a summary of the current character status (i.e., types, weights, etc.). Remember, if logging was turned on, the summary information displayed to your screen will also be saved to the log file. You may also choose to display a summary of the taxa (tstatus), the entire data matrix (showmatrix), and more. 6. INCLUDE AND EXCLUDE CHARACTERS PAUP* provides several ways to restrict analyses to a subset of the taxa and characters included in a data matrix. For example, the sample data set includes morphological and molecular characters. Suppose we wish to analyze only the morphological traits. These characters have already been identified in the sample file using the command charset (as charset morph). Character sets simplify certain procedures by allowing you to refer to a group of characters by a single name. You will start by excluding all characters in the data set except for the morphological characters. EXCLUDE all; [this excludes all characters, the charset “all” is automatically recognized by PAUP and does not need to be defined] INCLUDE morph; This includes all characters in a character set named “morph” defined in the nexus file you examined earlier, using the charset command. In other words, all molecular characters are now excluded. 7. DELETE AND RESTORE TAXA In the same way, you can define sets of taxa using the TAXSET command (see PAUP file in TextWrangler), and delete and restore them. DELETE fossils; [this deletes all taxa in the taxset fossils, defined using the TAXSET command in the nexus file] To restore these taxa – RESTORE fossils; You can also delete and restore single taxa by using their taxon name. 6 8. SET CHARACTER TYPES (unordered and ordered multistate) Morphological characters. By default, PAUP treats all multistate characters as unordered. However, if you wish to order multistate characters (012 etc), you can use the TYPESET and ASSUME commands. This command defines a typeset (named MorphoclineChars) that sets certain multistate characters as ordered – all other characters are the default, ie unordered.