[Bioperl-l] Re: Comparative genomics

[Daniel Barker]

On Fri, 28 Sep 2001, I wrote:

> > There are several matrix formats. The one I used/prefer was #NEXUS
> > format - used by several of the best pylogenetic (ie cladistic)
> > reconstruction programs like Paup. It has the facility to embed a
> > complete analysis configuration, data and the output in nested tree
> > descriptions.
>
> I prefer the more programmer-friendly PHYLIP formats, which are
> well-established and a sort of a "lowest common denominator" in that most
> phylogeny programs can at least import and export them. Also, I slightly
> disapprove of the way way Nexus lets you mix alignments, analysis and
> trees in the same file.

Apologies. After thinking about it more, I see the Nexus format has huge
advantages in the current context.

-- 
Daniel Barker.