linux phylogenetic tree software

[glen e. p. ropella-2]

Anyone know of a good linux/foss package for reading FASTA data files
and rendering trees?

--
glen e. p. ropella, 971-222-9095, http://agent-based-modeling.com


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[Leigh Fanning]

I was quite happy with this package for reading FASTA format:

http://cbl.sourceforge.net/

This might be useful towards tree rendering:

http://www.cs.unm.edu/~morin/sw.html

Leigh Fanning
Managing Member, Versiera, LLC



On Apr 30, 2009, at 12:30 PM, glen e. p. ropella wrote:


Anyone know of a good linux/foss package for reading FASTA data files
and rendering trees?

--
glen e. p. ropella, 971-222-9095, http://agent-based-modeling.com


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Meets Fridays 9a-11:30 at cafe at St. John's College
lectures, archives, unsubscribe, maps at http://www.friam.org



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[Marcus G. Daniels]

glen e. p. ropella wrote:
> Anyone know of a good linux/foss package for reading FASTA data files
> and rendering trees?.
>  
First you'll need to take your FASTA files get an alignment.   Good
packages for that are mafft and Muscle.

Then take your alignment infer your tree.   To do that, one good package
is PhyML.
  http://atgc.lirmm.fr/phyml/
PhyML isn't strictly speaking open source, but it's free.  

To actually draw a picture, an easy to use package is FigTree
  http://tree.bio.ed.ac.uk/software/figtree/

If you are an R user, I'd recommend the `ade4' and `ape' packages to do
related things.

Marcus

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[glen e. p. ropella-2]

Thanks to both of you for the suggestions.

Leigh Fanning emitted this, circa 30/04/09 12:03 PM:
> I was quite happy with this package for reading FASTA format:
>
> http://cbl.sourceforge.net/
>
> This might be useful towards tree rendering:
>
> http://www.cs.unm.edu/~morin/sw.html

Marcus G. Daniels emitted this, circa 30/04/09 12:06 PM:

> First you'll need to take your FASTA files get an alignment.   Good
> packages for that are mafft and Muscle.
>
> Then take your alignment infer your tree.   To do that, one good
> package is PhyML.
>
> http://atgc.lirmm.fr/phyml/
>
> PhyML isn't strictly speaking open source, but it's free.
>
> To actually draw a picture, an easy to use package is FigTree
> http://tree.bio.ed.ac.uk/software/figtree/

--
glen e. p. ropella, 971-222-9095, http://agent-based-modeling.com


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Meets Fridays 9a-11:30 at cafe at St. John's College
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