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PowerPC Mac versions of Phylip, fastDNAml & ClustalV available

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Tue Jun 21 11:37:34 EST 1994


PowerPC Macintosh versions of the following biology apps are 
available:

   PHYLIP (Phylogeny Inference Package) Version 3.5c 
     by Joseph Felsenstein 

   fastDNAml, version 1.0.6, 20 Nov 1992
     Gary Olsen & colleagues' souped up version of Felsenstein's dnaml     

   Clustal V  Multiple Sequence Alignments.
     by Des Higgins

- These are available by gopher or ftp to ftp.bio.indiana.edu,
in the IUBio-Software+Data/molbio/mac/0powermac/ folder.

- These are not official versions of the programs.  I just wanted to
make available PowerPC Macintosh versions of these.

- Programs are packaged as "fat" binaries, including both PowerPC
and 68000 binaries to run on either kind of Macintosh.


Tests of fastDNAml, using data "testdata_6.phylip" supplied with source.
 
Computers
  Intel 486 == Intel-clone 486 PC (AMD 80486 DX 20/40 MHz)
  Mac Q700  == Macintosh Quadra 700 (MC 68040 25/50 MHz)
  Mac PPC   == Macintosh PowerPC 601 (card in Q700, 25/50 MHz)
  Sparc 2   == Sun Sparcstation 2, Sparc CPU
  Sparc LX  == Sun Sparcstation LX, microSparc CPU 
              ( SPECint92 26.4, SPECfp92 21.0 )
  Sparc 10  == Sun SparcStation 10, model 41, SuperSparc CPU
              ( SPECint92 52.6, SPECfp92 64.7 )
	
Compilers
  BC  == Borland C 4.0 (Intel PC)
  CW  == MetroWerks CodeWarrior (Mac)
  GCC == GNU CC (Sun)
  MPW == Apple Macintosh Programmer's Workshop (Mac)
  SunCC == ancient, non-ansi bundled C compiler (Sun)
	
Computer & compilation method	        Execution time (seconds)	
  Mac Q700, unoptimized (CW)                             324.30
    (^ not using 68040 or FPU optimizations)
  Intel 486, optimized (BC)                              170.92
  Mac Q700, optimized (MPW) for 68040 w/FPU               63.95
  Sparc 2, unoptimized (SunCC)                            47.43
  Sparc 2, optimized (GCC)                                23.00
  Sparc LX, optimized (GCC)                               23.00
  Mac PPC, optimized (CW)                                 20.20
  Sparc 10, unoptimized (SunCC)                           10.32
	
	
	
For a comparison, the DNAML program from which fastDNAml was derived,
but a newer version 3.5c, takes ~40x longer to process the same data:

  dnaml 3.5c for Mac PPC, optimized (CW)                 785.26

	
-- 
-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu




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