Computational Sciences at AMNH

Contents

• Resources
   Mailing list
   Tutorials
   Repository
   Bugs
   Tests for Clusters

• Software
current
archival

• Sample Files
POY 4.0
POY 3.0

• Utilities

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

[Total downloads: 45416]

The development of POY4 is sponsored in part by CIPRES

Software

Current:

Version 4.1.1 ( 23 January 2009 ) [change history]
Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2009. POY 4.1.1. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

Binaries

• WinXP (single & parallel)

[download]

(Downloaded 533 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 259 times)

• Linux (single, x86)

[download]

(Downloaded 127 times)

Source Code

• Source Code

[download]

(Downloaded 122 times)

Documentation

• Documentation and sample datasets

[download]

(Downloaded 299 times)

Archival:

Version 4.1 ( 15 November 2008 ) [change history]
Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.1. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

Binaries

• WinXP (single & parallel)

[download]

(Downloaded 214 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 182 times)

• Linux (single, x86)

[download]

(Downloaded 76 times)

Source Code

• Source Code

[download]

(Downloaded 128 times)

Documentation

• Documentation and sample datasets

[download]

(Downloaded 337 times)

Version 4.0.2911 ( 7 October 2008 ) [change history]
Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2911. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

Binaries

• WinXP (single & parallel)

[download]

(Downloaded 311 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 156 times)

• Linux (single, x86)

[download]

(Downloaded 100 times)

Source Code

• Source Code

[download]

(Downloaded 142 times)

Documentation

• Documentation and sample datasets

[download]

(Downloaded 302 times)

Version 4.0.2885 ( 15 August 2008 ) [change history]
Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2885. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

Binaries

• WinXP (single & parallel)

[download]

(Downloaded 168 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 186 times)

• Linux (single, x86)

[download]

(Downloaded 122 times)

Source Code

• Source Code

[download]

(Downloaded 150 times)

Documentation

• Documentation and sample datasets

[download]

(Downloaded 207 times)

Version 4.0.2881 ( 17 July 2008 ) [change history]
Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2881. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

Binaries

• WinXP (single & parallel)

[download]

(Downloaded 229 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 208 times)

• Linux (single, x86)

[download]

(Downloaded 121 times)

Source Code

• Source Code

[download]

(Downloaded 139 times)

Documentation

• Documentation and sample datasets

[download]

(Downloaded 188 times)

Version 4.0.2870 ( 21 May 2008 ) [change history]
Citation

Varón, A., L. S. Vinh, I. Bomash, W. C.Wheeler. 2008. POY 4.0.2870. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php

Binaries

• WinXP (single & parallel)

[download]

(Downloaded 404 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 240 times)

• Linux (single, x86)

[download]

(Downloaded 137 times)

Source Code

• Source Code

[download]

(Downloaded 176 times)

Documentation

• Documentation and sample datasets

[download]

(Downloaded 283 times)

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 304 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 262 times)

• Linux (single, x86)

[download]

(Downloaded 167 times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 180 times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 238 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 278 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 228 times)

• Linux (single, x86)

[download]

(Downloaded 151 times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 166 times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 208 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 470 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 369 times)

• Linux (single, x86)

[download]

(Downloaded 201 times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 282 times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 362 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 297 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 242 times)

• Linux (single, x86)

[download]

(Downloaded 183 times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 191 times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 205 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 264 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 276 times)

• Linux (single, x86)

[download]

(Downloaded 180 times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 218 times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 231 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 282 times)

• Mac OS X (single & parallel)

[download]

(Downloaded 354 times)

• Linux (single, x86)

[download]

(Downloaded 0 times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 242 times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 303 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 283 times)

• Mac OS X (single CPU)

[download]

(Downloaded 320 times)

• Mac OS X (parallel)
Requires X11 libraries (see FAQ)

[download]

(Downloaded 286 times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 251 times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 275 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 194times)

• Mac OS X (single CPU)

[download]

(Downloaded 256times)

• Mac OS X (parallel)
Requires X11 libraries (see FAQ)

[download]

(Downloaded 255times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 199times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 204times)

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 253 times)

• Mac OS X (single CPU)

[download]

(Downloaded 314 times)

• Mac OS X (parallel)
Requires X11 libraries (see FAQ)

[download]

(Downloaded 279 times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 315 times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 266 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 370times)

• Mac OS X (single CPU)

[download]

(Downloaded 394times)

• Mac OS X (parallel)
Requires X11 libraries (see FAQ)

[download]

(Downloaded 342times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 277times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 365times)

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 380times)

• Mac OS X Intel (parallel)
Requires X11 libraries (see FAQ)

[download]

(Downloaded 354times)

• Mac OS X G4 + G5 (single CPU)

[download]

(Downloaded 352times)

• Mac OS X G4 + G5 (parallel)
Requires X11 libraries (see FAQ)

[download]

(Downloaded 327times)

Source Code

• Source Code for POY 4.0

[download]

(Downloaded 297times)

Documentation

• POY 4.0 Beta Documentation and sample datasets

[download]

(Downloaded 492times)

Version 3.0.11 [change history]

Binaries

• POY 3.0.11 for LINUX
(GCC 2.96; RedHat 7.3)

[download]

(Downloaded 418 times)

• POY 3.0.11 for LINUX
(GCC 3.2; RedHat 8.0)

[download]

(Downloaded 538 times)

• POY 3.0.11 for Mac OS X

[download]

(Downloaded 1039 times)

• POY 3.0.11 for Windows

[download]

(Downloaded 1725 times)

Source Code

• Source code for POY 3.0.11

[download]

(Downloaded 0 times)

Documentation

• POY Reference

[download]

(Downloaded 2873 times)

• Readme for POY 3.0.11

[download]

(Downloaded 1844 times)

Related software

• TCL/TK GUI for PC, Linux, Mac OS X

[download]

(Downloaded 626 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 387 times)

• POY 3.0 for Mac OS X

[download]

(Downloaded 366 times)

• POY 3.0 for Windows

[download]

(Downloaded 255 times)

Source Code

• Source code for POY 3.0

[download]

(Downloaded 362 times)

Documentation

• POY Reference

[download]

(Downloaded 2873 times)

• Readme for POY

[download]

(Downloaded 1298 times)

Related software

• TCL/TK GUI for PC, Linux, Mac OS X

[download]

(Downloaded 342 times)

Version 2.7

Binaries

• POY 2.7 for LINUX

[download]

(Downloaded 0 times)

• POY 2.7 for Windows

[download]

(Downloaded 343 times)

Source Code

• Source code for POY 2.7

[download]

(Downloaded 0 times)

Documentation

• POY Reference

[download]

(Downloaded 2873 times)

• Readme for POY

[download]

(Downloaded 1298 times)

Version 2.0

Bi naries

• POY 2.0 for LINUX

[download]

(Downloaded 859 times)

• POY 2.0 for Windows

[download]

(Downloaded 1298 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 340 times)

Documentation

• POY Reference

[download]

(Downloaded 2873 times)

• Readme for POY

[download]

(Downloaded 1298 times)

Sample Files

Sample Data
• Sample data for DOS	[download]	(Downloaded 1383 times)
• Sample data for LINUX	[download]	(Downloaded 873 times)
Sample Matricies
• Sample matricies	[download]	(Downloaded 1320 times)
Sample Output
• Sample output. Optional System requirements text.	[download]	(Downloaded 1211 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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