# Simulate an alignment

Section author: Gavin Huttley

For this example we just create a simple model using a four taxon tree with different branch lengths and a Felsenstein model.

Specify the 4 taxon tree,

Define our Felsenstein 1981 substitution model.

We’ll now create a simulated alignment of length 1000 nucleotides.

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Likelihood analysis of multiple loci

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Performing a parametric bootstrap