Questions tagged [substitution-model]
The substitution-model tag has no usage guidance.
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Estimating rate of evolution from a phylogeny
Any suggestions for the best way to estimate a metric for evolutionary rate of viral sequences of the same species?
I was using terminal branch length from a phylogeny and would quite like to try sub ...
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Single or partitioned model for supermatrix tree inference?
I am dealing with several genes in my dataset. For each of the genes, I have built gene tree, with their best estimated model. I am intended to look into the effect of the tree from concatenated ...
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Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?
I have a couple of prokaryotic genes that I'm trying to build phylogenetic trees from.
I inputted them into IQTree, which, as part of the workflow, runs through multiple substitution models until it ...
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File format of substitution matrix in clustalw
I need to set the substitution matrix used by command line CLUSTALW when comparing DNA sequences to:
0 -1 -1 -1
-1 0 -1 -1
-1 -1 0 -1
-1 -1 -1 0
from my ...
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How is the instantaneous rate of an instantaneous rate matrix determined?
In molecular evolution, I know that the instantaneous rate of the rate matrix is the limit of the rate as time approaches 0, but what I don't understand is how this rate is established or what I can ...
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