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Old 01-21-2013, 10:38 PM   #3
Location: Russia, Irkutsk

Join Date: Feb 2011
Posts: 40

Well, you use a bunch of methods and you get a bunch of different trees, that is usual. If you add, for instance, analysis of genomic rearrangements, you will get one more tree, some phenotypic traits will support yet another one and so on. So, pls do the following.
1) Give us some more details on analysis protocol, esp. on application of ML on 80% of genome (either I misunderstood you or it was incredibly computationally expensive) and on how exactly you built the SNP tree.
2) You don't mention whether you take into account horizontal gene transfer. If you do not, you surely must, because otherwise it may mislead your inference.
3) Consider using consensus tree or, better, consensus network for representing results, if everything else fails.
A_Morozov is offline   Reply With Quote