POY4 Quick StartWhat is POY4The structure of POY4 documentationRequirements: software and hardwareSoftwareHardwareObtaining and installing POY4Starting a POY4 sessionPOY4 interfaceNavigating the interfaceEntering commandsBrowsing the outputSwitching between the windowsInterrupting a processErrorsObtaining helpExitingWWW resourcesUsing POY4Importing dataInspecting dataBuilding initial treesPerforming a local searchSelecting treesVisualizing the resultsRunning scriptsKnown issuesPOY4 CommandsPOY4 Command StructureBrief DescriptionGrammar SpecificationNotationCommand Referencebuildcalculate_supportclear_memorycdechoexitfusehelpinspectloadperturbpwdquitreadrediagnoserecoverredrawrenamereportrunsavesearchselectsetstoreswaptransformuseversionwipePOY4 TutorialsBasic SearchAdvanced SearchFusing and RatchetingTrees and Step MatricesBremer SupportBootstrap SupportBootstrap Support with Static HomologiesChromosome AnalysisGeneral IndexPOY 3.0 Command Line IndexPOY 4.0 BetaQuickStart Guide and Program DocumentationVersion 4.0.1983Program and DocumentationAndr´es Var´onLe Sy VinhIllya BomashWard C. WheelerDocumentationIlya T¨emkinKurt M. PickettJuli´an FaivovichTaran GrantWilliam Leo SmithAndr´es Var´onDivision of Invertebrate Zoology, American Museum of Natural HistoryComputer Science Department, The Graduate School and University Center, TheCity University of New YorkLe Sy VinhWard C. WheelerIlya T¨emkinTaran GrantDivision of Invertebrate Zoology, American Museum of Natural HistoryKurt M. PickettDepartment of Biology, University of VermontJuli´an FaivovichDepartamento de Zoologia, Instituto de Biociˆencias, Universidade EstadualPaulistaWilliam Leo SmithDivision of Vertebrate Zoology, American Museum of Natural HistoryThe American Museum of Natural Historyc2007 by The American Museum of Natural HistoryAll rights reserved. Published 2007Var´on, A., L. S. Vinh, I. Bomash, W. C. Wheeler. 2007. POY 4.0.1983 Beta. NewYork, American Museum of Natural History. Documentation by Var´on, A., L. S.Vinh, I. Bomash, W. Wheeler, I. T¨emkin, K. M. Pickett, J. Faivovich, T. Grant,and W. L. Smith. http://research.amnh.org/scicomp/projects/poy.phpAvailable online at http://research.amnh.org/scicomp/projects/poy.php.Contents1 POY4 Quick Start 71.1 What is POY4 . . . . . . . . . . . . . . . . . . . . . . . . . . . 71.2 The structure of POY4 documentation . . . . . . . . . . . . . 81.3 Requirements: software and hardware . . . . . . . . . . . . . 81.3.1 Software . . . . . . . . . . . . . . . . . . . . . . . . . . 81.3.2 Hardware . . . . . . . . . . . . . . . . . . . . . . . . . 91.4 Obtaining and installing POY4 . . . . . . . . . . . . . . . . . . 91.5 Starting a POY4 session . . . . . . . . . . . . . . . . . . . . . . 121.6 POY4 interface . . . . . . . . . . . . . . . . . . . . . . . . . . . 141.7 Navigating the interface . . . . . . . . . . . . . . . . . . . . . 171.7.1 Ente ring com mands . . . . . . . . . . . . . . . . . . . 171.7.2 Browsing the output . . . . . . . . . . . . . . . . . . . 171.7.3 Switching between the windows . . . . . . . . . . . . . 171.7.4 Interrupting a process . . . . . . . . . . . . . . . . . . 181.8 Errors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181.9 Obtaining help . . . . . . . . . . . . . . . . . . . . . . . . . . 181.10 Exiting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201.11 WWW resources . . . . . . . . . . . . . . . . . . . . . . . . . 211.12 Using POY4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221.12.1 Importing data . . . . . . . . . . . . . . . . . . . . . . 221.12.2 Inspecting data . . . . . . . . . . . . . . . . . . . . . . 251.12.3 Building initial trees . . . . . . . . . . . . . . . . . . . 261.12.4 Performing a local search . . . . . . . . . . . . . . . . 281.12.5 Selecting trees . . . . . . . . . . . . . . . . . . . . . . 291.12.6 Visualizing the results . . . . . . . . . . . . . . . . . . 301.12.7 Running scripts . . . . . . . . . . . . . . . . . . . . . . 311.12.8 Known issues . . . . . . . . . . . . . . . . . . . . . . . 3334 CONTENTS2 POY4 Commands 352.1 POY4 Command Structure . . . . . . . . . . . . . . . . . . . . 352.1.1 Brief Description . . . . . . . . . . . . . . . . . . . . . 352.1.2 Grammar Specification . . . . . . . . . . . . . . . . . . 362.2 Notation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382.3 Command Reference . . . . . . . . . . . . . . . . . . . . . . . 392.3.1 build . . . . . . . . . . . . . . . . . . . . . . . . . . . . 392.3.2 calculate support . . . . . . . . . . . . . . . . . . . . . 412.3.3 clear memory . . . . . . . . . . . . . . . . . . . . . . . 462.3.4 cd . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 462.3.5 echo . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472.3.6 exit . . . . . . . . . . . . . . . . . . . . . . . . . . . . 482.3.7 fuse . . . . . . . . . . . . . . . . . . . …
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