Friday, November 23, 2007

storing phylogenetic trees in mx

Turkey in belly I've sat down to flesh out the storage of phylogenetic trees in mx. Krishna's phylo_tree lexer/parser creates nice Ruby objects of newick formatted trees, all I had to do was incorporate another of his efforts better_nested_set, to translate the parsed tree to a database table, all in all just a couple lines of new code. Visualization is another can of worms. I think I'll likely wait till a nice Rails/Ruby graph (as in trees) generator comes out before attempting this. As a thought experiment its interesting to think about how to display a tree completely in ascii, and not just drawing the branches with _, -, and |, but rather displaying groups of terminals, or labeled internal nodes in some meaningful manner depending on where you are in the tree. Its late, so I envision starting with something like "you are in twisty set of passages all alike" ...

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