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Old 08-27-2013, 11:23 PM   #5
Location: Russia, Irkutsk

Join Date: Feb 2011
Posts: 40

Perhaps you could just extract informative sites and use just them like SNPs, since computational burden of analyzing megabases via ML or bayesian inference is tremendous, and most sequence doesn't carry any information anyway.
Also, the "concatenate contigs (in whatever order and strand orientation they happen to be in assembly) and map reads of other isolates on resulting sequence" part doesn't look really cool. I'm not sure if gene calling and therefore distinguishing neutral vs non-neutral SNPs will be reliable with such and approach. In addition, it throws away all data on real gene order, which can be valuable phylogenetic marker, and imposes a semi-artifactual one.

PS: what's the point in creating several nearly identical threads? Bump it if nobody answers in a couple of weeks or so.

Last edited by A_Morozov; 08-27-2013 at 11:25 PM.
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