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PHYLIPPhylogeny Inference PackageVersion 3.695April, 2013by Joseph FelsensteinDepartment of Genome Sciences and Department of BiologyUniversity of Washingtonaddress:Department of Genome SciencesBox 355065Seattle, WA 98195-5065USAE-mail address: joe (at) gs.washington.eduContents of This DocumentContents of This DocumentA Brief Description of the ProgramsCopyright Notice for PHYLIPThe Documentation Files and How to Read ThemWhat The Programs DoRunning the Programs A word about input files Installing a recent version of Oracle Java Running the programs on a Windows machine Running the programs on a Macintosh with Mac OS X Running the programs on a Unix or Linux system Running the programs on a Macintosh with Mac OS 8 or 9 (deprecated) Running the programs in MSDOS Running the Drawgram and Drawtree Java interfaces Running the Drawgram and Drawtree Java GUI interfaces in Windows Running the programs in background or under control of a command file An example (Unix, Linux or Mac OS X) Subtleties (in Unix, Linux, or Mac OS X) An example (Windows) Testing for existence of files Prototyping keyboard response filesPreparing Input Files Input and output files Where the files are Data file formatThe MenuThe Output FileThe Tree FileThe Options and How To Invoke Them Common options in the menu The U (User tree) option The G (Global) option The J (Jumble) option The O (Outgroup) option The T (Threshold) option The M (Multiple data sets) option The W (Weights) option The option to write out the trees into a tree file The (0) terminal type optionThe Algorithm for Constructing Trees Local rearrangements Global rearrangements Multiple jumbles Saving multiple tied trees Strategy for finding the best treeA Warning on Interpreting ResultsRelative Speed of Different Programs and Machines Relative speed of the different programs Speed with different numbers of species Relative speed of different machinesGeneral Comments on Adapting the Package to Different Computer SystemsCompiling the programs Unix and Linux On Windows systems Compiling with Cygnus Gnu C++ Compiling with Microsoft Visual C++ Macintosh Compiling with GCC on Mac OS X with our Makefile Compiling with GCC on Mac OS X with X Windows What aboutthe Metrowerks Codewarrior compiler VMS VAX systems Parallel computers Other computer systems Compiling the Java interfacesFrequently Asked Questions How to make it do various things Background information needed: Questions about distribution and citation: Questions about documentation Additional Frequently Asked Questions, or: "Why didn't it occur to you to ... (Fortunately) obsolete questionsNew Features in This VersionComing Attractions, Future PlansEndorsements From the pages of Cladistics ... in the pages of other journals: ... and in the comments made by users when they register:References for the Documentation FilesCreditsOther Phylogeny Programs Available Elsewhere PAUP* MrBayes MEGA PAML Phyml RAxML TNT DAMBEHow You Can Help MeIn Case of TroubleA Brief Description of the ProgramsPHYLIP, the Phylogeny Inference Package, is a package of programs forinferring phylogenies (evolutionary trees). It has been distributed since1980, and has over 30,000 registered users, making it the most widelydistributed package of phylogeny programs. It is available free, fromits web site: is available as source code in C, and also as executables forsome common computer systems. It can infer phylogenies by parsimony,compatibility, distance matrix methods, and likelihood. It can alsocompute consensus trees, compute distances between trees, draw trees,resample data sets by bootstrapping or jackknifing, edit trees, andcompute distance matrices. It can handle data that are nucleotidesequences, protein sequences, gene frequencies, restriction sites,restriction fragments, distances, discrete characters, and continuouscharacters.Copyright Notice for PHYLIPThe following copyright notice is intended to cover all source code, alldocumentation, and all executable programs of the PHYLIP package. Copyright 1980-2013. University of Washington. Allrights reserved. Permission is granted to reproduce, perform, and modifythese programs and documentation files. Permission is granted to distributeor provide access to theseprograms provided that this copyright notice is not removed, the programs arenot integrated with or called by any product or service that generatesrevenue, and that your distribution of these documentation files and programsare free. Any modifiedversions of these materials that are distributed or accessible shall indicatethat they are based on these programs. Institutions of higher education aregranted permission to distribute this material to their students and stafffor a fee to recover distribution costs. Permission requests for any otherdistribution of these programs should be directed to license (at) u.washington.edu .The Documentation Files and How to Read ThemPHYLIP comes with an extensive set of documentation files. Theseinclude the main documentation file (this one), which you should readfairly completely. In addition there are files for groups of programs,including ones for the molecular sequenceprograms, the distance matrixprograms, thegene frequency and continuous charactersprograms, the discrete characters programs,and the tree drawing programs. Finally,each program has its own documentation file. References for thedocumentation files are all gathered together in this main documentationfile. A good strategy is to:Read this main documentation file.Tentatively decide which programs are of interest to you.Read the documentation files for the groups of programs thatcontain those.Read the documentation files for those individual programs.There is an excellent guide to using PHYLIP 3.6 also available. It was written byJarno Tuimala of the Center for Scientific Computing in Espoo, Finland and isavailable as a PDF here. It is alsodistributed at the main PHYLIP web site.What The Programs DoHere is a short description of each of the programs. For more detaileddiscussion you should definitely read the documentation file for theindividual program and the documentation file for the group of programsit is in. In this list the name of each program is a link which willtake you to the documentation file for that program. Note that there is noprogram in the PHYLIP package called PHYLIP.CliqueFinds the largest clique of mutually compatible characters, and the phylogeny which they recommend, for discrete character data with two states. The largest clique (or all cliques within a given size range of the largest one) are found by a very fast branch and bound search method. The method does not allow for missing data. For such cases the T (Threshold) option of Pars or Mix may be a useful alternative. Compatibility methods are particular useful when some characters are of poor quality and the rest of good quality, but when it is not known in advance which ones are which.ConsenseComputes consensus trees by the majority-rule consensus tree method, which also allows one to easily find the strict consensus tree. Is not able to compute the Adams consensus tree. Trees are input in a tree file in standard nested-parenthesis notation, which is produced by many of the tree estimation programs in the package. This program can be used as the final step in doing bootstrap analyses for many of the methods in the package.ContmlEstimates phylogenies from gene frequency data by maximum likelihood under a model in which all divergence is due to genetic drift in the absence of new mutations. Does not assume a molecular clock. An alternative method of analyzing this data is to compute Nei's genetic distance and use one of the distance matrix programs. This program can also do maximum likelihood analysis of continuous characters that evolve by a Brownian Motion model, but it assumes that the characters evolve at equal rates and in an uncorrelated fashion, so that it does not take into account the usual correlations of characters.ContrastReads a tree from a tree file, and a data set with continuous characters data, and produces the independent contrasts for those characters, for use in any multivariate statistics package. Will also produce covariances, regressions and correlations between characters for those contrasts. Can also correct for within-species sampling variation when individual phenotypes are available within a population.DnacompEstimates phylogenies from nucleic acid sequence data using the compatibility criterion, which searches for the largest number of sites which could have all states (nucleotides) uniquely evolved on the same tree. Compatibility is particularly appropriate when sites vary greatly in their rates of evolution, but we do not know in advance which are the less reliable ones.Dnadist Computes four different distances between species from nucleic acid sequences. The distances can then be used in the distance matrix programs. The distances are the Jukes-Cantor formula, one based on Kimura's 2- parameter method, the F84 model used in Dnaml, and the LogDet distance. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites in a prespecified way, and also according to a Hidden Markov model. The program can also make a table ofDnainvarFor nucleic acid sequence data on four species, computes Lake's and Cavender's phylogenetic invariants, which test alternative tree topologies. The program also tabulates the frequencies of occurrence of the different nucleotide patterns. Lake's invariants are the method which he calls "evolutionary parsimony".Dnaml Estimates phylogenies from nucleotide sequences by maximum likelihood. The model employed allows for unequal expected frequencies of the four nucleotides, for unequal rates of transitions and transversions, and for different (prespecified) rates of change in different categories of sites, and also use of a Hidden Markov model of rates, with the program inferring which sites have which rates. This also allows gamma-distribution and gamma-plus-invariant sites distributions of rates across sites.DnamlkSame as Dnaml but assumes a molecular clock. The use of the two programs together permits a likelihood ratio test of the molecular clock hypothesis to be made.DnamoveInteractive construction of phylogenies from nucleic acid sequences, with their evaluation by parsimony and compatibility and the display of reconstructed ancestral bases. This can be used to find parsimony or compatibility estimates by hand. DnaparsEstimates phylogenies by the parsimony method using nucleic acid sequences. Allows use the full IUB ambiguity codes, and estimates ancestral nucleotide states. Gaps treated as a fifth nucleotide state. It can also do transversion parsimony. Can cope with multifurcations, reconstruct ancestral states, use 0/1 character weights, and infer branch lengths.DnapennyFinds all most parsimonious phylogenies for nucleic acid sequences by branch-and-bound search. This may not be practical (depending on the data) for more than 10-11 species or so.DollopEstimates phylogenies by the Dollo or polymorphism parsimony criteria for discrete character data with two states (0 and 1). Also reconstructs ancestral states and allows weighting of characters. Dollo parsimony is particularly appropriate for restriction sites data; with ancestor states specified as unknown it may be appropriate for restriction fragments data.DolmoveInteractive construction of phylogenies from discrete character data with two states (0 and 1) using the Dollo or polymorphism parsimony criteria. Evaluates parsimony and compatibility criteria for those phylogenies and displays reconstructed states throughout the tree. This can be used to find parsimony or compatibility estimates by hand. DolpennyFinds all most parsimonious phylogenies for discrete-character data with two states, for the Dollo or polymorphism parsimony criteria using the branch-and-bound method of exact search. May be impractical (depending on the data) for more than 10-11 species. DrawgramPlots rooted phylogenies, cladograms, circular trees and phenograms in a wide variety of user-controllable formats. The program is interactive. It has an interface in the Java language which gives it a closely similar menu on all three major operating systems. Final output can be to a file formatted for one of the drawing programs, for a ray-tracing or VRML browser, or one at can be sent to a laser printer (such as Postscript or PCL-compatible printers), on graphics screens or terminals, on pen plotters or on dot matrix printers capable of graphics. Many of these formats are historic so we no longer have hardware to test them. If you find a problem please report it.DrawtreeSimilar to Drawgram but plots unrooted phylogenies. It also has aJava interface for previews.FactorTakes discrete multistate data with character state trees and produces the corresponding data set with two states (0 and 1). Written by Christopher Meacham. This program was formerly used to accomodate multistate characters in Mix, but this is less necessary now that Pars is available.FitchEstimates phylogenies from distance matrix data under the "additive tree model" according to which the distances are expected to equal the sums of branch lengths between the species. Uses the Fitch-Margoliash criterion and some related least squares criteria, or the Minimum Evolution distance matrix method. Does not assume an evolutionary clock. This program will be useful with distances computed from molecular sequences, restriction sites or fragments distances, with DNA hybridization measurements, and with genetic distances computed from gene frequencies.GendistComputes one of three different genetic distance formulas from gene frequency data. The formulas are Nei's genetic distance, the Cavalli-Sforza chord measure, and the genetic distance of Reynolds et. al. The former is appropriate for data in which new mutations occur in an infinite isoalleles neutral mutation model, the latter two for a model without mutation and with pure genetic drift. The distances are written to a file in a format appropriate for input to the distance matrix programs.KitschEstimates phylogenies from distance matrix data under the "ultrametric" model which is the same as the additive tree model except that an evolutionary clock is assumed. The Fitch-Margoliash criterion and other least squares criteria, or the Minimum Evolution criterion are possible. This program will be useful with distances computed from molecular sequences, restriction sites or fragments distances, with distances from DNA hybridization measurements, and with genetic distances computed from gene frequencies. MixEstimates phylogenies by some parsimony methods for discrete character data with two states (0 and 1). Allows use of the Wagner parsimony method, the Camin-Sokal parsimony method, or arbitrary mixtures of these. Also reconstructs ancestral states and allows weighting of characters (does not infer branch lengths).MoveInteractive construction of phylogenies from discrete character data with two states (0 and 1). Evaluates parsimony and compatibility criteria for those phylogenies and displays reconstructed states throughout the tree. This can be used to find parsimony or compatibility estimates by hand. NeighborAn implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method. Neighbor Joining is a distance matrix method producing an unrooted tree without the assumption of a clock. UPGMA does assume a clock. The branch lengths are not optimized by the least squares criterion but the methods are very fast and thus can handle much larger data sets.ParsMultistate discrete-characters parsimony method. Up to 8 states (as well as "") are allowed. Cannot do Camin-Sokal or Dollo Parsimony. Can cope with multifurcations, reconstruct ancestral states, use character weights, and infer branch lengths.PennyFinds all most parsimonious phylogenies for discrete-character data with two states, for the Wagner, Camin-Sokal, and mixed parsimony criteria using the branch-and-bound method of exact search. May be impractical (depending on the data) for more than 10-11 species. PromlEstimates phylogenies from protein amino acid sequences by maximum likelihood. The PAM, JTT, or PMB models can be employed, and also use of a Hidden Markov model of rates, with the program inferring which sites have which rates. This also allows gamma-distribution and gamma-plus-invariant sites distributions of rates across sites. It also allows different rates of change at known sites.PromlkSame as Proml but assumes a molecular clock. The use of the two programs together permits a likelihood ratio test of the molecular clock hypothesis to be made.ProtdistComputes a distance measure for protein sequences, using maximum likelihood estimates based on the Dayhoff PAM matrix, the JTT matrix model, the PBM model, Kimura's 1983 approximation to these, or a model based on the genetic code plus a constraint on changing to a different category of amino acid. The distances can also be corrected for gamma-distributed and gamma-plus-invariant-sites-distributed rates of change in different sites. Rates of evolution can vary among sites in a prespecified way, and also according to a Hidden Markov model. The program can also make a table of percentage similarity among sequences. The distances can be used in the distance matrix programs.ProtparsEstimates phylogenies from protein sequences (input using the standard one-letter code for amino acids) using the parsimony method, in a variant which counts only those nucleotide changes that change the amino acid, on the assumption that silent changes are more easily accomplished. percentage similarity among sequences.RestdistDistances calculated from restriction sites data or restriction fragments data. The restriction sites option is the one to use to also make distances for RAPDs or AFLPs.RestmlEstimation of phylogenies by maximum likelihood using restriction sites data (not restriction fragments but presence/absence of individual sites). It employs the Jukes-Cantor symmetrical model of nucleotide change, which does not allow for differences of rate between transitions and transversions. This program is very slow.RetreeReads in a tree (with branch lengths if necessary) and allows you to reroot the tree, to flip branches, to change species names and branch lengths, and then write the result out. Can be used to convert between rooted and unrooted trees, and to write the tree into a preliminary version of a new XML tree file format which is under development and which is described in the Retree documentation web page.SeqbootReads in a data set, and produces multiple data sets from it by bootstrap resampling. Since most programs in the current version of the package allow processing of multiple data sets, this can be used together with the consensus tree program Consense to do bootstrap (or delete-half-jackknife) analyses with most of the methods in this package. This program also allows the Archie/Faith technique of permutation of species within characters. It can also rewrite a data set to convert it from between the PHYLIP Interleaved and Sequential forms, and into a preliminary version of a new XML sequence alignment format which is under development and which is described in the Seqboot documentation web page.ThreshmlReads a tree from a tree file, and a data set with discrete 0/1 characters. Using the threshold model of quantitative genetics, the program runs a Markov Chain Monte Carlo (MCMC) sampler to sample the underlying continuous characters (the liabilities) that cause the discrete characters. The covariances of the liabilities are estimated, as well as the transformation from the liabilities to underlying independently evolving characters.Treedist Computes the Branch Score distance between trees, which allows fordifferences in tree topology and which also makes use of branch lengths. Alsocomputes another distance by Robinson and Foulds that uses branch lengths,and the Symmetric Difference distance between trees, whichallows for differences in tree topology but does not use branch lengths.Running the ProgramsThis section assumes that you have obtained PHYLIP as compiled executables(for Windows, Mac OS X, or Linux), or else you have obtained the source codeand compiled it yourself (for Linux, Unix, Mac OS X, or Windows).For the programs Drawtree and Drawgram you will also need a recent version of Java installed on your computer to run them interactively.Note that for machines forwhich compiled executables are available, there will usually be no need foryou to have a compiler or compile the programs yourself. This sectiondescribes how to run the programs. Later in this document we willdiscuss how to download and install PHYLIP (in case you arereading this without yet having done that). Normally you will only readyour copy of the documentation files after downloading and installing PHYLIP.After describing the input files, we will describe how to run most ofthe programs onWindows, Mac OS X, Linux, and Unix systems). After that, we will givespecial descriptions of the interactive Java interface for the tree-drawingprograms Drawgram and Drawtree, including how to run these interfaces onWindows, Mac OS X, and Linux systems. These may require you todownload and install on your computer the most recent version of OracleJava, which is available from Oracle at no cost. We describe this below afterdiscussing input files.A word about input files.For all of these types of machines, it isimportant to have the input files for the programs (typically data files)prepared in advance. They can be prepared in any editor, but it is importantthat they be saved in Text Only ("flat ASCII") format, not in the format thatword processors such as Microsoft Word want to write (in Microsoft Word,make sure that the data encoding used is "US ASCII", as using any of theUnicode codings can cause trouble). It is up to you to readthe PHYLIP documentation files which describe the files formats that areneeded. There is a partial description in the next section of this document.The input files can also be obtained by running a program thatproduces output files in PHYLIP format (some of these programs do, and so doprograms by others such as sequence alignment programs such as ClustalW andsequence format conversion programs such as Readseq). There is not anyinput file editor available in any program in PHYLIP (you should notsimply start running one of the programs and then expect to click a mousesomewhere to start creating a data file). When they start running, the programs look first for input files withparticular names (such as infile, treefile, intree, or fontfile).Exactly which file names they look for varies a bit from program to program,and you should read the documentation file for the particular program tofind out. If you have files with those names the programs will use themand not ask you for the file name. If they do not find files of thosenames, the programs will say that they cannot find a file of that name, andask you to type in the file name.For example, if Dnaml looksfor the file infile and does not find one of that name,it prints the message:dnaml: can't find input file "infile"Please enter a new file name>This does not mean that an errorhas occurred. All you need to do is to type in the name of the file. (Joe, you need to rewrite or eliminate this paragraph, it is too condescending)The program looks for the input files in the same folder that theprogram is in (a folder is the same thing as a "directory"). In Windows, Mac OS X, Linux, or Unix, if you are asked for thefile name you can type in the path to the file, as part of the name (thus,if the file is in the folder containing the current folder, you can type ina file name such as ../myfile.dna). If you do not know what a"folder" is, or what "above" means, then you are a member of the newgeneration who just clicks the mouse and assumes that a list of file nameswill magically appear. (Typically members of this generation have no ideawhere the files are on their system, and accumulate enormous amounts ofunnecessary clutter in their file systems.) In this case you should asksomeone to explain folders to you.Running the programs on a Macintosh with Mac OS XWe have provided a Mac OS X version of the executables, in the form of"universal binaries" that should run either on PowerMac or Intel iMacsystems (to ensure that they will run on both 32-bit and 64-bitMac OS X systems, we have made sure that we compiled theexecutables as 32-bit executables). The programs can berun by clicking on their icons. They open a Terminal window, and themenu appears in it. Note that after the program is finished, the Terminalwindow remains open, and operations can be done in it. You will have toclose the window yourself if you don't want it. The programs can beterminated by typing control-C (press down the "control" key in thelower-left corner of the keyboard and type "c").It is also possible to run the executables from within aTerminal window by typing the program name, but this is a little harder.You will find the Terminal utility available in the Utilities folder in theApplications folder.You do need to have links made in the exe folder to theprograms. This can be done the first time you need them, by enteringthe exe folder and opening a Terminal window, and then typingsource linkmac. This creates the proper links, and thereafteryou do not need to do this again. The programs can be run by typingtheir names in a Terminal window whose current working directory isexe The programs work well this way,though the programs Drawgram and Drawtree may be slow toopen and close plotting windows.The programs can be terminated by typing control-C or byclosing the Terminal window by using the red button in the upper-leftcorner of the window.One problem we have often encountered using Mac OS X is that it is possible fordata files to have the wrong kind of characters at the ends of their lines.They may have carriage-return (ASCII/ISO 13 or control-M) characters at theends of their lines when they should instead have the Unix newline character(ASCII/ISO 10 or control-J) there. This can happen with files transferredfrom other operating systems or files produced in some word processors.It results in segmentation-fault or memory errors. If you encounter these,check this possibility carefully.If you normally run Mac OS X applications using open -a, you may need to use the command lsregister -f -r /your/path/to/apps. You can find it with the command locate lsregister.Running the programs on a Unix or Linux system.Type the name of the programin lower-case letters (such as dnaml). To terminate the program whileit is running, type Control-C (which means to press down on the Ctrl keywhile typing the letter C).On some systems you may need to type ./ before the program name,so that in the above case it would be ./dnaml. This is mostlyneeded if the user's PATH does not include their current directory, somethingwhich is often done as a security precaution.Running the programs on a Macintosh with Mac OS 8 or 9 (deprecated)We no longer produce and distribute Mac OS 8 and Mac OS 9 executablesof the Phylip programs, as we no longer have access to these operatingsystems to produce and test them. As a last resort, onlyif you do not have access to a system that will run the current distribution, you have two choices:fetch and run out of date Mac OS 8 / OS 9 executables, orattempt to compile the current source with the Metrowerks compiler.Once you have the executables, you may follow the directions below.Double-click on the icon forthe program. A window should open. Further dialog with the program occursby typing on the keyboard in response to what you see in the window. Theprograms can be terminated by usingthe mouse to open the File menu in the upper-left corner of the program'swindow area and then select Quit. Alternatively, you can use theCommand-Q key combination.When you use Quit, the program will ask you whether you want to savea file whose name is the program name (often followed by .out -- forexample, if you are using Dnaml it will ask you if you want to save fileDnaml.out. This file is simply a record of everything thatdisplayed on the program window, and you usually will not want to save it.Pressing the Enter key or selecting the Do Not Save button withthe mouse will keep this from being saved.If you encounter memory limitations on a Mac OS 8 or 9 Macintosh,and determine thatthis is not due to a problem with the format of the input file, as itoften will be, you may be able to solve it by raising the limits of thestack and heap sizes of the program. To do this click on the programand then select Get Info from the Finder File menu.This will open a window which can be made to show the memory limitsof the program. These can be changed by selecting them and typing inlarger numbers. This may relieve nagging memory problems. If it doesnot, consult your local documentation and suspect problems with yourinput file format.Running the Drawgram and Drawtree Java interfacesWith version 3.695 we have released an interactive Java interface for the tree-drawing programs, Drawgram and Drawtree. The reason is that the graphic interface language for Mac OS X has changed from the Carbon GUIto the Cocoa GUI, which would require a lot of rewriting of code. The alternative X11 (X Windows) GUI machinery on Mac OS X hasbeen deprecated by Apple, and is showing its age on Linux systems.Looking at available options, it seemed best to use Java to construct GUIinterfaces, as this could be done in a reasonably compatible way across allthree major platforms. There are disadvantages too -- to get fullcompatibility we need to ask users to download the most recent availableJava from its maker, Oracle. That is not difficult but is a tiresome extrastep. Oracle owns Java, and Java is not public-source, but there seems to beno sign that Oracle is going to make Java runtime machinery unavailableor charge for it.Not all Java implementations will run PHYLIP's Drawgram and DrawtreeGUIs. A reasonably compatible Java is distributed with Mac OS X, but noJava is distributed along with Windows, and the Java distributed withLinux distributions is unfortunately not compatible enough with ourJava GUI. So for these two platforms you will need to download Oracle Java. Wewill give you instructions for that below.The new GUI for Drawgram and Drawtree is a testbed for a general set of GUIinterfaces for all our programs, which will be present in version 4.0 whenthat is distributed, which will be soon. The work you do to put a recentversion of Oracle Java on your system will make using version 4.0 easier.For people who use Drawgram or Drawtree in a "pipeline" run by shell scripts,there should be no interruption in your ability to do that. The current C code for those programs can either be called by the Java GUIor be run froma command line or a shellscript (for which see below). Almost all of thefeatures of Drawgram and Drawtree are available from their character-modemenu when run that way, except for the interactive previewing of plots. Wehope that the shell scripts will still work and will not need modificationfor this version of PHYLIP.Running the Drawgram and Drawtree Java GUI interfaces in WindowsTo run the Drawgram or Drawtree programs, you find the Drawgram.jar orDrawtree.jar files, which are Java Archive files in our folder ofexecutable programs. You can run themby clicking on their icons. Detailed instructions for using theinterfaces are given in the general documentation file for tree-drawingprograms draw.html (which you should read), and the documentation files for thetwo programs drawgram.htmland drawtree.html. Installing a recent version of Oracle JavaTo run the interactive interfaces of the tree-drawing programs Drawgram andDrawtree, you need to have an appropriate version of Java installed on yourcomputer. If you have Java installed, you should test whether it is anappropriate version by trying to run Drawgram or Drawtree (for this youwill need an input tree file present as well). Is it likely that youhave a compatible Java on your system On a Mac OS X systems you are likely to have an compatible versionof Java. On Windows systems no Java implementation is installed by default. You candownload a recent Oracle Java on your Windows system by using this link and following the instructionsthere. On some Linux systems there are Java installations which are notcompatible with our Java interfaces. This is the result of licensingissues. You can remedy the situation by downloading a recent Oracle Javaversion and installing it: On Debian-based Linux systems such as Ubuntu and Linux Mint, youcan download Java from this link and install it. If you do not have administrator privileges onthe Linux system, you can install it in your own folders. On Linux systems that use ther RPM package management system (includingRed Hat, Fedora, SUSE, and Mandriva) you can use theseinstructions from Oracle to install Java, but you must have administratorprivileges on your Linux system.Once a useable version of Java is installed, you do not have to repeat theinstallation every time you run one of the programs Drawgram or Drawtree.Running the programs on a Windows machine.Double-click on the icon forthe program. A window should open with a menu in it. Further dialog with theprogram occursby typing on the keyboard in response to what you see in the window. Theprograms can be terminated either by typing Control-C (which means topress down on the Ctrl key while typing the letter C), or by usingthe mouse to open the File menu in the upper-left corner of the program'swindow area and then select Quit. Other than this, most PHYLIP programsmake no use of the mouse. The tree-drawing programs Drawtree and Drawgramdo allow use of the mouse to select some options.The programs open a window for their menus. This window may be too small foryour tastes. They can be resized by tugging on the lower-right corner of thewindow. In addition, the font may be too small. On most versions of Windows,you can click on the small C:\ iconsymbol at the upper-left corner of the window, and choose theProperties menu choice there. One of its tab options allows youto change the font and size ofthe print. I prefer large font sizes such as 16x12.The programs can also be run in a Command Prompt window under Windows, in much the same way as they were under the MSDOS operating system, which is what theCommand Prompt window emulates. Command Prompt windows can be open bychoosing that option in the Accessories menu which is in the All Programs menu.Once in the Command Prompt window, make sure that you are in thecorrect folder, using the cd command as needed to find the folderwhere the executable PHYLIP programs are. Then type the name of the programthat you want to use in lower-case letters (such as dnaml). To terminate the program whileit is running, type Control-C (which means to press down on the Ctrl keywhile typing the letter C). Running the programs in background or under control of a command fileIn running the programs, you may sometimes want to put them in backgroundso you can proceed with other work. On systems with a windowing environmentthey can be put in their own window, and commands like the Unix and Linuxnice command used to makethem have lower priority so that they do not interfere with interactiveapplications in other windows. This part of the discussion willassume either a Windows system or a Unix or Linux system. I willnote when the commands work on one of these systems but not the other.Mac OS X is actually Unix (surprise! surprise!) and you canrun PHYLIP programs in background on any Mac OS X system by simply followingthe instructions for Unix, using a terminal window to do so if necessary.(The Terminal utility can be found in the Utilities folder which isinside the Applications folder).If there is no windowing environment, or if you want to make PHYLIP programspart of a larger workflow of some sort, on a Unix or Linux system you will want to use anampersand (&) after the command file name when invoking it to put thejob in the background. You will have to put all the responses to theinteractive menu of the program into a file and tell the background jobto take its input from that file (we cover this below).On Windows systems there is no & or nice commandbut input and output redirection and command files work fine in a Commmandwindow. A command file can either be invoked by clicking on its icon orby typing its name from a Command Prompt window. The a file of commands must have a name ending in .bat or .cmd, such as foofile.bat. You can run the batch file from a Command window by typing its name (such asfoofile) without the .bat.Here are examples, for the different operating systems:An example (Unix, Linux or Mac OS X)Here is an example for Windows, Linux, or using a Terminal window ofMac OS X. Below you will find a separate example for Windows. If youare using Windows you should read that section instead.Suppose you want to run Dnaml in a background, taking itsinput data from a file called sequences.dat, putting its interactiveoutput to file called screenout, and using a file called input asthe place to store the interactive input. The file input need onlycontain two lines:sequences.datYwhich is what you would have typed to run the program interactively, inresponse to the program's request for an input file name if it did notfind a file named infile, in response the the menu.To run the program in background, in Unix or Linux you would simply give the command:dnaml < input > screenout &These run the program with input responses coming from input andinteractive output being put into file screenout. The usual outputfile and tree file will also be created by this run (keep that in mindas if you run any other PHYLIP program from the same directory whilethis one is running in background you may overwrite the output file fromone program with that from the other!).Subtleties (in Unix, Linux, or Mac OS X)If you wanted to give the program lower priority, so that it wouldnot interfere with other work, and you have Berkeley Unix type job controlfacilities in your Unix or Linux (and you usually do), you can use thenice command:nice +10 dnaml < input > screenout &which lowers the priority of the run. To also time the run and put thetiming at the end of screenout, you can do this:nice +10 ( time dnapars < input ) >& screenout &which I will not attempt to explain.On Unix or Linux systemsyou may also want to explore putting the interactive output into thenull file /dev/null so as to not be bothered with it (but then youcannot look at it to see why something went wrong). If you have problemswith creating output files that are too large, you may want toexplore carefully the turning off of options in the programs you run.If you are doing several runs in one, as for example when you do abootstrap analysis using Seqboot, Dnapars (say), and Consense, youcan use an editor to create a "command file" with these commands:seqboot < input1 > screenoutmv outfile infilednapars < input2 >> screenoutmv outtree intreeconsense < input3 >> screenoutThe command file might be named something likefoofileIt must be givenexecute permission by using the command chmod +x foofile.The job that foofile describescan be run in background on Unix or Linux by giving the commandfoofile &Note that you must also have the interactive inputcommands for Seqboot (including the random number seed), Dnapars, andConsense in the separate files input1, input2, and input3.An example (Windows)If you have a Windows system and want to run Dnaml in a background, taking itsinput data from a file called sequences.dat, putting its interactiveoutput to file called screenout, and using a file called inputasthe place to store the interactive input. The file input need onlycontain two lines:sequences.datYwhich is what you would have typed to run the program interactively, inresponse to the program's request for an input file name if it did notfind a file named infile, in response the the menu.To run the program in background, you can place the commanddnaml < input > screenout &in a file called something like foofile.bat. This "batch file" thathas commands and has its name end in .bat or .cmdcan be run simply by double-clicking on the file icon, which will usuallyhave a picture of a gear. A Command Prompt windows (an MSDOS window) will thenopen and the commands in the batch file will be run in it. Alternatively,you can open a Command Prompt window yourself. It will be found in theAll Programs menu, as one of the options under Accessories. Make sure thatafter it opens, you tell it to change its working directory to the one thathas the batch file in it.The batch file with this command runs the program with input responses coming from input andinteractive output being put into file screenout. The usual outputfile and tree file will also be created by this run (keep that in mindas, if you run any other PHYLIP program from the same directory whilethis one is running in background, you may overwrite the output file fromone program with that from the other!).Testing for existence of filesNote also that when PHYLIP programs attempt to open a new output file (such asoutfile, outtree, or plotfile, if they seea file of that name already in existence they will ask you if you want tooverwrite it, and offer alternatives including writing to another file,appending information to that file, or quitting the program without writing tohe file. This means that in writing batch files it is important to knowwhether there will be a prompt of this sort. You must know in advancewhether the file will exist. You may want to put in your batch file acommand that tests for the existence of a pre-existing output file andif so, removes it, such as these commands in Unix, Linux, or Mac OS X:if test -e fubarfilethen rm fubarfilefiYou might even want to put in a command that creates afile of that name, so that you can be sure it is there! Either way,you will then know whether to put into your file of keyboard responses theproper response to the inquiry about overwriting that output file.Offhand, I do not know how to test for the existence of files in Windows, butI suspect that there is a way.Prototyping keyboard response filesMaking the proper files of keyboard responses for use with commandfiles is most easily done if you prototype the process by simplyrunning the program and keeping a careful record of the keyboardresponses that you need to give to get the program to run properly.Then create a file in an editor and type those keyboard responses intoit. Thus if the program requires that you answer a question aboutwhat to do with the output file with a keyboard response of R,then wants you to type a menu selection of U (to have it use a User tree),then wants you to answer Y to end the menu, and another R to tell it toreplace the output file, you would have the file of keyboard responsesbeRUYRSince when you run the program interactively, each keyboardresponse is ended by pressing the Enter key on your keyboard,in the file of keyboard responses you must end each line aftertyping the appropriate character.Testing the keyboard responses with an interactive run willbe essential to having batch runs succeed.Preparing Input FilesThe input files for PHYLIP programs must be prepared separately - there isno data editor within PHYLIP. You can use a word processor (or texteditor) to prepare them yourself, or you can use a program that producesa PHYLIP-format output.With the 3.695 release of Phylip we have included a directory called TestData whichcontains the data used to generate the examples shown in the individual program html pagesand the output files they produce. Within this TestData directory there is a subdirectory that has the name of the program (for example contrast) and within that there are the filescontrastinfile.txt, contrastintree.txt and contrastoutfile.txt. If you look at the Contrast documentation you can see infile, intree, and outfile mentioned in the example. The testdata/contrast/*.txt files exactly match those in the example, so if you wish to experiment with Contrast you have both a good infile and a good intree and the outfile expected from the example, if you set your conditions to match the example.Sequence alignment programs such as ClustalWcommonly have an option to produce PHYLIP files as output, and someother phylogeny programs, such as MacClade and TreeView, are capable ofproducing a PHYLIP-format file.It is very important that the input files be in "Text Only" or "ASCII" format. This means that they contain only printable ASCII/ISOcharacters, and not any unprintable characters. Many word processors suchas Microsoft Word save their files in a format that contains unprintablecharacters, unless you tell them not to. In the Microsoft Word family ofword processors, the first time you edit a file, when you go to Savein the File menu,the file the program will instead do a Save As function, and ask youin what format you want the file to be written. If you are using Microsoft Word, chose Plain Text. A box willopen (or on the Mac OS X version of Word, an Option button will beavailable) in which you can chosen the setting US-ASCII. Thesettings that start with Western European also should work. None ofthe other encodings are likely to work. If you are using WordPad, chose Text Document (*.txt). Donot chose Unicode Text Document. If you are using Notepad, chose Text Document and then choseANSI in the list of encoding methods, but not Unicodeor UTF8 in the list of encodings.If you are on Mac OS X and using its own document editor TextEdit,you may need to use the Make Plain Text choice in the Format menu.Once that is done, TextEdit also has a checkbox in the Save Aswindow that defaults to providing a .txt extension at the end of thefile name -- if you don't want that to happen, uncheck that box.Save As also may have a check box that defaults to hiding the three-letter extension of the file, sothat when the file is saved as (say) foofile.txt its name will appear to not have the extension .txt at the end of the file name, even though it really is there. It is best to uncheck that box.For these word processors, the next time you edit the same file, using Save, the program should use those settings without asking you. If you have some trouble getting an input file that the programs can read, look into whether you properly set these options. This can be usually be done by using the Save As choice in the File menu and making the right settings.Text editors such as the vi and emacs editors onUnix and Linux (and available on Mac OS X too), or the picoeditor that comes with the pinemailer program, produce their files in Text Only format and should notcause any trouble.The format of the input files is discussed below, and you should alsoread the other PHYLIP documentation relevant to the particular type ofdata that you are using, and the particular programs you want to run, asthere will be more details there.Input and output filesFor most of the PHYLIP programs, information comes from a series ofinput files, and ends up in a series of output files: ------------------- infile ---------> intree ---------> -----------> outfile weights --------> program -----------> outtree categories -----> -----------> plotfile fontfile -------> ------------------- 59ce067264






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