Questions tagged [substitution-model]

The tag has no usage guidance.

Filter by
Sorted by
Tagged with
0 votes
1 answer

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 ...
web's user avatar
  • 11
1 vote
1 answer

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 ...
Laura's user avatar
  • 869
1 vote
1 answer

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 ...
gcorso's user avatar
  • 159
0 votes
0 answers

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 ...
Namenlos's user avatar
  • 317