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POY (Phylogenetic Analysis of DNA and other Data using Dynamic Homology)

[Total downloads: 27510]

Visit the POY4 mail group to post questions and bugs and find information on using POY.

The development of POY4 is sponsored in part by project

CIPRES (Cyberinfrastructure for Phylogenetic Research)

Software

Current:
Version 4.0 Beta Build 2635 ( 11 March 2008 ) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 2635. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
 
• WinXP (single & parallel)
 [download] (Downloaded 134 times)
 
• Mac OS X (single & parallel)
[download]
(Downloaded 97 times)
 
• Linux (single, x86)
[download]
(Downloaded 35 times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 49 times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 87 times)
Version 4.0 Beta Build 2602 ( 8 February 2008 ) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 2602. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
 
• WinXP (single & parallel)
 [download] (Downloaded 147 times)
 
• Mac OS X (single & parallel)
[download]
(Downloaded 90 times)
 
• Linux (single, x86)
[download]
(Downloaded 28 times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 44 times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 83 times)
Version 4.0 Beta Build 2398 ( 23 October 2007 ) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 2398. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
  • WinXP [download] (Downloaded 327 times)
 
• Mac OS X (single & parallel)
[download]
(Downloaded 236 times)
 
• Linux (single, x86)
[download]
(Downloaded 82 times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 163 times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 234 times)
Version 4.0 Beta Build 2318 ( 12 October 2007 ) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 2318. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
  • WinXP [download] (Downloaded 80 times)
 
• Mac OS X (single & parallel)
[download]
(Downloaded 104 times)
 
• Linux (single, x86)
[download]
(Downloaded 53 times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 69 times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 79 times)
Version 4.0 Beta Build 2205 ( 10 September 2007 ) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 2205. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
  • WinXP [download] (Downloaded 137 times)
 
• Mac OS X (single & parallel)
[download]
(Downloaded 135 times)
 
• Linux (single, x86)
[download]
(Downloaded 59 times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 94 times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 109 times)
Version 4.0 Beta Build 1983 ( 18 July 2007 ) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 1983. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
  • WinXP [download] (Downloaded 161 times)
 
• Mac OS X (single & parallel)
[download]
(Downloaded 220 times)
 
• Linux (single, x86)
[download]
(Downloaded 0 times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 121 times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 181 times)
Version 4.0 Beta Build 1908 (12 June 2007) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 1908. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
  • WinXP [download] (Downloaded 157 times)
 
• Mac OS X (single CPU)
[download]
(Downloaded 188 times)
 
• Mac OS X (parallel)
Requires X11 libraries (see FAQ)
[download]
(Downloaded 161 times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 127 times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 157 times)


Version 4.0 Beta Build 1902 (11 June 2007) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 1902. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
  • WinXP [download] (Downloaded 78times)
 
• Mac OS X (single CPU)
[download]
(Downloaded 132times)
 
• Mac OS X (parallel)
Requires X11 libraries (see FAQ)
[download]
(Downloaded 125times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 73times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 73times)


Version 4.0 Beta Build 1822 (16 May 2007) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 1822. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
  • WinXP [download] (Downloaded 127 times)
 
• Mac OS X (single CPU)
[download]
(Downloaded 175 times)
 
• Mac OS X (parallel)
Requires X11 libraries (see FAQ)
[download]
(Downloaded 155 times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 112 times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 142 times)


Version 4.0 Beta Build 1724 (29 March 2007) [change history]
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 1724. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
  • WinXP [download] (Downloaded 251times)
 
• Mac OS X (single CPU)
[download]
(Downloaded 253times)
 
• Mac OS X (parallel)
Requires X11 libraries (see FAQ)
[download]
(Downloaded 205times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 151times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 231times)

Version 4.0 Beta Build 1665 (17 February 2007)
Citation
Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2007. POY 4.0 Beta 1665. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
 

 

Binaries
  • WinXP [download] (Downloaded 320times)
 
• Mac OS X Intel (single CPU)
[download]
(Downloaded 237times)
 
• Mac OS X Intel (parallel)
Requires X11 libraries (see FAQ)
[download]
(Downloaded 218times)
 
• Mac OS X G4 + G5 (single CPU)
[download]
(Downloaded 218times)
 
• Mac OS X G4 + G5 (parallel)
Requires X11 libraries (see FAQ)
[download]
(Downloaded 197times)
 

 

Source Code
  • Source Code for POY 4.0
 [download] (Downloaded 174times)
 

 

Documentation
  • POY 4.0 Beta Documentation and sample datasets [download] (Downloaded 354times)

 

Version 3.0.11 [change history]
  Binaries
  • POY 3.0.11 for LINUX
(GCC 2.96; RedHat 7.3)		 [download] (Downloaded 296 times)
 
• POY 3.0.11 for LINUX
(GCC 3.2; RedHat 8.0)
[download]
(Downloaded 409 times)
 
• POY 3.0.11 for Mac OS X
[download]
(Downloaded 909 times)
 
• POY 3.0.11 for Windows
[download]
(Downloaded 1582 times)
 

 

Source Code
  • Source code for POY 3.0.11 [download] (Downloaded 0 times)
 

 

Documentation
  • POY Reference [download] (Downloaded 2565 times)
 
• Readme for POY 3.0.11
[download]
(Downloaded 1658 times)
 

 

Related software
  • TCL/TK GUI for PC, Linux, Mac OS X [download] (Downloaded 503 times)
 

 

Version 3.0
 

Binaries
  • POY 3.0 for LINUX
For use in parallel "poy.linux" can be renamed, but the same name must be used for all spawned binaries		 [download] (Downloaded 238 times)
 
• POY 3.0 for Mac OS X
[download]
(Downloaded 243 times)
 
• POY 3.0 for Windows
[download]
(Downloaded 255 times)
 

 

Source Code
  • Source code for POY 3.0 [download] (Downloaded 245 times)
 

 

Documentation
  • POY Reference [download] (Downloaded 2565 times)
 
• Readme for POY
[download]
(Downloaded 1112 times)
 

 

Related software
  • TCL/TK GUI for PC, Linux, Mac OS X [download] (Downloaded 213 times)
 

 

Version 2.7
  Binaries
  • POY 2.7 for LINUX
 [download] (Downloaded 0 times)
 
• POY 2.7 for Windows
[download]
(Downloaded 226 times)
 

 

Source Code
  • Source code for POY 2.7 [download] (Downloaded 0 times)
 

 

Documentation
  • POY Reference [download] (Downloaded 2565 times)
 
• Readme for POY
[download]
(Downloaded 1112 times)
 

 

Version 2.0
  Bi naries
  • POY 2.0 for LINUX [download] (Downloaded 683 times)
 
• POY 2.0 for Windows
[download]
(Downloaded 1112 times)
 

 

Source Code
  • Base source code for POY 2.0 [download] (Downloaded 0 times)
 
• Parallel source code for POY 2.0
Requires pvm and ocaml to compile. pvm is available from ftp://netlib2.cs.utk.edu/pvm3
ocaml is available from ftp://ftp.inria.fr
[download]
(Downloaded 217 times)
 

 

Documentation
  • POY Reference [download] (Downloaded 2565 times)
 
• Readme for POY
[download]
(Downloaded 1112 times)

 

Sample Files


Sample Data
  • Sample data for DOS [download] (Downloaded 1144 times)
 
• Sample data for LINUX
[download]
(Downloaded 810 times)
 

 

Sample Matricies
  • Sample matricies [download] (Downloaded 1092 times)
 

 

Sample Output
  • Sample output.
Optional System requirements text.		 [download] (Downloaded 1000 times)

 

Utilities

jack2hen
Converts POY output (one or more trees in nested parentheses format) into a matrix (in hennig format) of group inclusion characters representing the concensus tree used for contraint files.
 

 

Binaries
  • jack2hen for Windows [download] (Downloaded 0 times)
 

 

Source Code
  • jack2hen source code [download] (Downloaded times)

 
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