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wedAM.txt
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wedAM.txt
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Sue and Big cats in CA
# do you care to look at genome rearrangements rather than SNPs?
# how do you quantify these changes in a phylogeny?
# how do you (A) detect recombination from sequence data; and (B) how does a virus actually facilitate recombination?
4944567884
10000116
cycles going to take about 6.5 hours
########
is it possible to create own matrix? say non-symmetric? (ex. penalize AT --> CG less than CG --> AG)
is it possible to define different matricies? (ex. if you see pairs or triplets of errors, perhaps those are likely due to sequencing error and should be less costly)
when you have 3 nodes in a tree... or 2 nodes... or N nodes....
how are you splitting up the number of site Likelihood scores? where do you break it up? is it at every node?
how do you fit that back into an alignment?
... what's the relationship between:
- the number of nodes
- the number of positions in an alignment
- the number of individuals
among-side rate heterogenerity: 3 options
looks for invariant sites...may be a functional/structural component that is under selection, so you can't change
looks for site-specific rates... look at rate changes on a site-by-site basis
looks at gamma model which uses an alpha parameter (which is the shape of the distribution) to model the distribution of rate change
- for this last one, a big alpha == normal distribution of rate changes...
- for small alpha (say 0.5), then basically some sites change extremely fast, some sites change very slowly
among the models:
GTR = general time reversible == each site changes independently
I = some sites are invariant
gamma = weird R greek symbol