PAUP*: Phylogenetic Analysis Using Parsimony (and Other Methods) 4.0 Beta
Sinauer Associates 公司的PAUP* 是目前使用最廣泛的演化分析軟體,其讀作Paup Star,而PAUP是Phylogenetic Analysis Using Parsimony 的縮寫。
PAUP*是一款用於構建進化樹(系統發育樹)並進行相關檢驗的軟體,包含了眾多分子演化模型和方法,可利用最大似然法、簡約法、距離法等方法分析分子數據(DNA、蛋白質序列)、形態學數據及其他類型的數據(如行為學數據)。該軟件主要用於演化生物學研究,也可用於生態學和法醫學研究。
PAUP* version 4.0 is a major upgrade and new release of the software package for inference of evolutionary trees, for use in Macintosh, Windows, UNIX/VMS, or DOS-based formats. The influence of high-speed computer analysis of molecular, morphological and/or behavioral data to infer phylogenetic relationships has expanded well beyond its central role in evolutionary biology, now encompassing applications in areas as diverse as conservation biology, ecology, and forensic studies. The success of previous versions of PAUP: Phylogenetic Analysis Using Parsimony has made it the most widely used software package for the inference of evolutionary trees. In addition, the PAUP manual has proven to be an essential guide, serving as a comprehensive introduction to phylogenetic analysis for beginning researchers, as well as an important reference for experts in the field. With the inclusion of maximum likelihood and distance methods in PAUP* 4.0, the new version represents a great improvement over its predecessors. In addition, the speed of the branch-and-bound algorithm has been enhanced and a number of new features have been added, from agreement subtrees to tests for combinability of data and permutation tests for nonrandomness of data structure. These, along with many other improvements, will make PAUP* 4.0 an even more indispensable tool in comparative biological analysis than were previous editions of the program and manual. PAUP* 4.0 and MacClade 3 use a common data file format (NEXUS), allowing easy interchange of data between the two programs.
- Full support for tree searching under DNA maximum-likelihood and distance-based optimality criteria (in addition to parsimony).
- Automatic estimation of maximum-likelihood model parameters, either on specified trees or during tree searches. A wide range of DNA substitution models are available, including the most general reversible model and its submodels (Jukes-Cantor, Kimura 2P, HKY85, F84 used in DNAML and fastDNAml, Tamura-Nei). Among-site rate variation can be accommodated using gamma-distributed rates, an unknown fraction of invariable-sites, site-specific rates, or a combination of these.
- Estimation of evolutionary distances under a full set of reversible models, including "custom" distances that can be tailored to any restriction of the most general reversible model and the LogDet distance. Distances can be corrected for among-site rate variation using gamma and invariable-sites models (or both).
- Neighbor-joining, quartet-puzzling, star-decomposition and UPGMA tree-searching algorithms (in addition to stepwise addition and branch-swapping of earlier versions).
- Calculation of "agreement subtrees" (largest common pruned trees) showing the largest subset of taxa for which all trees in a set agree upon relationships.
- Jackknife resampling analysis under all optimality criteria (in addition to bootstrap).
- Parametric and nonparametric tests for significant differences between trees (Kishino-Hasegawa, Templeton, winning-sites).
- Printing of unrooted trees and support for printing large trees across multiple pages (Macintosh version only).
- Tree-searching and evaluation under Goloboff's "implied weights" parsimony criterion.
- Partition-homogeneity (incongruence length-difference) test for evaluating homogeneity of subsets of characters (e.g., between genes, or between molecular and morphological characters).
- Estimation of ancestral nucleotides using maximum likelihood.
- "Portable interface" version for DOS (including MS Windows), VMS, and Unix operating systems.
PAUP*最開始只是為蘋果Macintosh系統設計;後來才有Windows平台,Windows版本只有一個簡單的用戶界面;另外還有設計給Unix/Linux系統使用的版本,但只有命令行界面。所以目前總共有三種版本,介紹如下:
PAUP* for MAC
只能用於Mac 晶片的蘋果電腦,如果蘋果電腦使用的是Intel的晶片,就只能用命令列模式運行該軟體。
The Macintosh version of PAUP* 4.0 is the most full-featured implementation currently available. Users may choose between command-line and menu-driven interfaces to implement all of the available functions. PAUP* 4.0 also provides a scroll back display buffer, a versatile editor, command recall, and high-resolution tree printing/saving options. PAUP* 4.0 for Mac is available for four Macintosh architectures: Power Macintosh (Altivec), Power Macintosh (PPC), Apple Macintosh (68K), and Apple Macintosh without a floating point unit (68K noFPU).
OS X compatibility:
The Altivec and PPC versions of PAUP will run under the classic layer of Mac OS X. Starting with the forthcoming release of Beta 11, Mac users will be given a choice to install a command-line version of PAUP* in addition to the classic Mac GUI version. The command-line version runs on Mac OS X in a terminal window and takes full advantage of Mac OS X's memory protection and preemptive multitasking but LACKS a Graphical User Interface (GUI). Work is currently underway to "carbonize" the GUI Mac version of PAUP*; however, at this time, we cannot speculate on when this version will be available.
Power Macintosh (Altivec)
- System software (Mac OS) 9.x to 10.3 (Classic)
- A minimum of 4 MB RAM
- 2 MB of available hard-disk space
Power Macintosh (PPC)
- System software (Mac OS) version 7 to 10.3 (Classic)
- A minimum of 4 MB RAM
- 2 MB of available hard-disk space
68K and 68K noFPU
- System software (Mac OS) version 6.0.4 to 8.x
- A minimum of 4 MB RAM
- 2 MB of available hard-disk space
68K - for Apple Macintosh machines that have at least a 68020 processor and that either have a floating-point coprocessor or a processor with an onboard floating-point unit (MC68881/MC68882). This includes the majority of machines made for 68030 and 68040 processors (Quadra, Centris) and most Macintosh II class CPUs.
68K noFPU - for Apple Macintosh machines based on the 68LC040 processor which do not have a floating-point coprocessor (e.g., PowerBook 500 series, many LC, Performa, pre-Mac II models, and some Centris models). The "noFPU" version will run on any 68K Mac, but it will perform much more slowly than the FPU version on systems that have floating-point units.
PAUP* for PC (windows)
The Windows version runs as a "GUI" application, however, unlike the Macintosh version most options are command-line-driven. The advantage to running PAUP* under Windows is that a scrollback display buffer is built into the program, an editor is provided, and commands are remembered between sessions (they can be recalled, edited, etc.).
Note: PAUP* 4.0 Windows Interface does not print or save high-resolution trees.
System Requirements -- Windows Interface
- 386, 486, Pentium series. Note: PAUP will only run on a machine that has a numeric data processor (NDP) either on the main processor (e.g., 486 and pentium series) or a coprocessor (e.g., 80387 with 80386 or 80487SX with 80486SX ).
- Windows 95, 98, ME, NT, 2000, and, XP.
- A minimum of 4 MB of RAM. Note: More memory may be required for larger data sets.
- 2 MB of available hard-disk space.
PAUP* for Linux/Unix
The "Portable Version" of PAUP* 4.0 is written and will be distributed in ANSI C. PAUP* will run on most platforms (architecture/OS) provided the source is compiled using an appropriate C compiler.
Note: PAUP* 4.0 Portable Version does not print or save high-resolution trees.
Before the final release of Version 4.0 we are making a set of UNIX/VMS beta executables available for the following platforms:
- Alpha/Unix (OSF1, Digital UNIX, Tru64 UNIX)
- Alpha/VMS
- Alpha/Linux
- PPC/Linux
- PPC/Mac OS X (this is not a carbonized application; it is command-line only)
- RS6000/AIX
- SGI/Irix (MIPS II and MIPS III)
- SPARC - UltraSPARC/Solaris
- x86/Linux
- Possibly others on request
Versions of PAUP* are available for most common platforms (Architecture/OS). Each version is capable of performing the same analyses, however, only the Macintosh versions can access all of the commands and setting via menus. Click on the version listed below to get a more detailed description of available features and system requirements.
Versions
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Architecture
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Operating System
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Macintosh
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PAUP Altivec
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Power Macintosh with Altivec (G4)
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Mac System 9.0 or higher
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PAUP PPC
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Power Macintosh (PPC)
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Mac System 7 or higher
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PAUP 68k
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Apple Macintosh (68k)
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Mac System 6.0.4 or higher
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PAUP 68k No FPU
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Apple Macintosh (68k noFPU)
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Mac System 6.0.4 or higher
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PC(Windows)
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PAUP Windows interface
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x86
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Windows 95, 98, ME, NT, 2000, XP
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PAUP windows console
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x86
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Windows 95, 98, ME, NT, 2000, XP
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UNIX
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PAUP Portable
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Many RISC and CISC
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Systems with a C compiler.
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Macintosh OS X Leopard (GUI version; universal binaries):
Note: After extracting the downloaded file (if necessary), you may need to right-click the icon and choose Open the first time (to get around the warning that the application is from an unknown developer).
Mountain Lion and later (OS X 10.8+; compiled with icc)
Note regarding font issues on OS X: Some users have reported that PAUP* refuses to launch (particularly after upgrading to El Capitan), complaining that the "Required font "MesloLGS-Regular" was not found in the application package." This probably indicates corruption in the system font tables rather than a problem with the PAUP* application bundle. A fix that has consistently worked is to kill the "fontd" process using the Activity Monitor program. This process will be automatically restarted and will rebuild the font tables, and PAUP* will now launch successfully.
Windows GUI version:
This version now officially requires Windows 7 (either 32- or 64-bit), but probably runs under Vista as well. (If you are running Vista, I highly recommend that you update to at least Windows 7.) There may be a few as-yet-undiscovered glitches in the dialog boxes, so please report these if you encounter them.
Win32 version
Command-line binaries:
Note: After gunzip'ing the downloaded file (if necessary), you may need to make it executable using a command like chmod a+x paup4a164_osx_leopard.
Mac OS X:
Mountain Lion and later (10.8+)
Windows:
No separate command-line version is needed. Just download and run the installer for the GUI version. A console (command-line) version will also be installed, and can be run by entering "paup" at a command prompt.
Intel Linux:
Choose a flavor that works for you. These binaries should work on other Linux distributions as well, but let me know ([email protected]) if you can't get them to run.
Centos/RedHat 64-bi
Ubuntu 64-bit
Also, note that these command-line versions need the Fortran runtime library to be available. If the program does not start due to a missing library, try installing the GFortran compiler (or something that will install the needed library, such as R, LAPACK, or Octave).