[Biopython-dev] Phylogenetic rats nests( oops I meant trees )

[Cayte]

Many of the bioformats represent phylogenetic data as well as sequence or path data.  I can think of a number of problems with
phylogenetic data.

1.  A number of types of relationships are possible.  A sequence may be a descendent or an ancestor of another sequence.
They both may have a common ancestor.  They may have converged to the same patteern.  They may have hopped across species.  Whatever the arguments against transgenic species, the assertion that it never happens in nature ain'tr so!  The latest issue of Natural History describes how the vertebrate immune system may have once been a parasite.

2.  Researchers often don't agree among themselves what these relationships are.  Should the links contain epistemology links that describe the level of confidence and the methodology plus journal references?

3.  Links will change as new research unfolds.  This will be a maintenance issue( luckily not ours ).  But we need the ability to easily change links and remove dead links.  Should a mechanism for the storage historical information be provided?

4. What if an intermediate is found between an ancestor descendent pair? Should we delete the old link?  Then the annotation will be lost.  Should the old link contain pointers to the new links?

5.  Should we limit our scope to just seuences?

Please share your thoughts on this.

                                                                 Cayte
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