[BioRuby] Phylogenetic Trees or Hierarchical Clustering

[Naohisa GOTO]

Hi,

I always use phylogenetic tree construction software such as
PHYLIP and MEGA4, and I don't know much about the pure Ruby
solutions. Below are found by using Google search.

There are some pure Ruby implementations of clustering algorithms,
though I haven't used them.

AI4R (Artificial Intelligence for Ruby):
http://ai4r.rubyforge.org/

clusterer: http://rubyforge.org/projects/clusterer/

I found a phylogenetic tree visualization implementation written
in JRuby, and I found it can also work with normal Ruby 1.8.7.

Egan A et al. (2008)
IDEA: Interactive Display for Evolutionary Analyses.
BMC Bioinformatics 2008, 9:524
http://www.biomedcentral.com/1471-2105/9/524
http://ideanalyses.sourceforge.net/

Thanks,

Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Mon, 1 Mar 2010 16:42:25 -0500
Jillian E Kozyra <jillyh0 at gmail.com> wrote:

> Dear Colleagues,
> 
> We are working on a linguistics project in which we will calculate language
> similarities. From the language similarity matrix, we would like to create
> either a hierarchical clustering output or phylogenetic tree. We seek a pure
> Ruby plugin with which to do this. Could you give us some guidance?
> 
> Thanks,
> Jillian
> 
> -- 
> 917-434-7511
> http://sswl.railsplayground.net
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby