File: Using_Seq-Gen_with_PAUP

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seq-gen 1.3.5-2
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Seq-Gen by Andrew Rambaut and Nick Grassly

Equivalent commands in PAUP and Seq-Gen:

PAUP												Seq-Gen
===================================================================================
lset nst=2 variant=hky tratio=2.0;					-mhky -t2.0

lset nst=6 rmat=(1.0 2.0 3.0 4.0 5.0);				-mrev -r1.0,2.0,3.0,4.0,5.0,1.0

charpartition codon=1st:1-.\3,2nd:2-.\3,3rd:3-.\3;	-c0.3,0.2,2.5

charpartition genes=RNA:1-300,CDS:301-1000;			-p3 (plus rates in treefile)