PhyloCoco
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Minimalist tool for molecular phylogenetics.   Free
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PhyloCoco is a minimalist tool for molecular phylogenetics able to rebuild phylogenies by means of the likelihood criterion. Phylococo automatically selects the best substitution model of DNA evolution for the dataset of sequences to be analyzed and display after a short time the best so far phylogeny found.

PhyloCoco features:
PhyloCoco implements the algorithms described in [D. Catanzaro, R. Pesenti and M. C. Milinkovitch. Estimating phylogenies under maximum likelihood: a very large-scale neighborhood approach. Submitted to BMC Bioinformatics. Currently under second
What's New
Version 2.3: Release notes were unavailable when this listing was updated.
Requirements
Intel/PPC, A G4 or an Intel Core Duo processor; Mac OS X 10.4 or later, Java 1.4 or later Recommended: an Intel Core 2 Duo, Mac OS X 10.5.3 or later, Java 1.5 or later



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PhyloCoco User Discussion (Write a Review)
ver. 2.x:
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burypromote

+15
umijin had trouble on 17 Nov 2007
Doesn't work on my Intel MacMini with Leopard. It won't even open the test file.

Idea sounds great though.
[Version 1.0d]

7 Replies

burypromote
- (developer) replied on 19 Nov 2007
Yes, this can happen. The computational core is compiled under mac os 10.4.10 and it is untested on Leopard.

As soon the new version for OS 10.5 will be released.
burypromote
- (developer) replied on 28 May 2008
Please check your CPU type. In fact, the code is compiled specifically for an intel core 2 duo (the processor of a macbook pro to be precise). Maybe that's the problem.
burypromote

+403
MacUpdate-Lon replied on 28 May 2008
To the developer: The application is stated to be a Universal binary when a 'Get Info' command is issued against the application.
burypromote
- (developer) replied on 28 May 2008
Right, but this only for the graphical application. The external executables are strongly optimized for the intel core 2 duo.
burypromote

+15
umijin replied on 13 Jun 2008
OK, so please make that point clear in the product description.

And consider making it at least functional on core duos, as not all of us have core 2.
burypromote

+45
Dalahast replied on 19 Jun 2008
And still others (me) are perfectly happy running Leopard on their PPC iBook G4s they got a while before the Macbooks even existed.
burypromote
- (developer) replied on 19 Jun 2008
PhyloCoco 2.2 run on any processor now.

Please note however that the ppc and x86 generic code is still not so optimized as the one for intel core 2 duo.

We are working hard to release new optimized computational cores. Thanks for the patience.
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Downloads:1,617
Version Downloads:521
Type:Education : Science
License:Free
Date:05 Aug 2009
Platform:PPC 32 / Intel 32 / OS X
Price:Free0.00
Overall (Version 2.x):
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PhyloCoco is a minimalist tool for molecular phylogenetics able to rebuild phylogenies by means of the likelihood criterion. Phylococo automatically selects the best substitution model of DNA evolution for the dataset of sequences to be analyzed and display after a short time the best so far phylogeny found.

PhyloCoco features:
PhyloCoco implements the algorithms described in [D. Catanzaro, R. Pesenti and M. C. Milinkovitch. Estimating phylogenies under maximum likelihood: a very large-scale neighborhood approach. Submitted to BMC Bioinformatics. Currently under second revision] and hereafter summarized:

  • The GTR model of DNA evolution.
  • Random Directions, Brent's algorithm and Random Search for unconstrained non-linear optimization of the likelihood parameters.
  • Very Large Scale Neighborhood (VLSN) search for the topology optimization.
  • Iterated Local Search (ILS) to explore the solution space.
PhyloCoco uses figtree to display the resulting phylogeny.


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