[BioRuby] Alignment plugin

Peter biopython at maubp.freeserve.co.uk
Mon Apr 26 17:56:26 UTC 2010

On Mon, Apr 26, 2010 at 6:25 PM, Rutger Vos <rutgeraldo at gmail.com> wrote:
> What you describe below is not what I meant, though it's also very
> important w.r.t. preserving the provenance of annotations. We're
> thinking in a number of different directions and so the requirements
> are starting to creep in :-)
> What I meant is, by long-winded example, the following: imagine you're
> studying the phylogeny of lemurs, and you want to look at
> morphological and behavioral characters. Here's what a character state
> matrix might look like:
> D._madagascariensis - 0
> H._aureus 4 1
> H._simus 6 ?
> H._griseus ? 1
> The first column captures the number of teeth in the lower-jaw
> toothcomb. Some lemurs use the incisors of the lower jaw as a grooming
> apparatus, and they have (I believe) either 4 or 6 teeth in that
> "comb". D._madagascariensis does not have this apparatus at all, so
> its state for this column could be coded as "-", conceptually a bit
> like a gap in an alignment, interpreted as "does not apply".

Or perhaps as a zero?

> To some extent, a matrix with such characters would be like an
> alignment, and in many cases you would analyze this data using the
> same tools for phylogenetic inference, like paup, phylip, mrbayes,
> etc. Also, the same data formats (nexus/nexml, phylip) describe both
> these matrices and alignments.

In these file format, am I right in thinking the non-sequence based
characteristics are all still encoded by single letters? e.g. single
digits. If so, that still allows the data to be held as simple strings.


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