[Bioperl-l] Phylogenetic networks.

Alexey Morozov alexeymorozov1991 at gmail.com
Wed Jun 13 02:27:48 EDT 2012


Sup colleagues. I think we could use a couple of things.
First, the phylogentic networks. Not the interaction/regulation networks
(which is implemented), but generalization of concept of tree (see eg D.
Huson et al "Phylogenetic networks: concepts, algorithms and
applications"). Seems like network object may inherit from Bio::Tree,
though actually it's other way around, and then several objects like splits
(aka bifurcations) and maybe some others can be necessary.
Second, dealing with genomic rearrangements: at least IO, like writing
GRIMM- or MGR-compatible files from genomic RichSeqs, maybe distance
metrics and other simple algorithms.
I see that both are pretty obscure phylogenetic toys, but they still might
get useful.

Alexey Morozov
LIN SB RAS


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