I wish to estimate transition/transversion ratio per each tree branch. I tried PAML baseml but got estimations only for some of the my MSAs. Can someone recommend another way to calculate it?

Thanks

seqfile = seq

treefile = tree

outfile = out

noisy = 9 * 0,1,2,3: how much rubbish on the screen
verbose = 1 * 1: detailed output, 0: concise output

runmode = 0 * 0: user tree; 1: semi-automatic; 2: automatic

```
* 3: StepwiseAddition; (4,5):PerturbationNNI
```

model = 4 * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85

```
* 5:T92, 6:TN93, 7:REV, 8:UNREST, 9:REVu; 10:UNRESTu
```

Mgene = 0 * 0:rates, 1:separate; 2:diff pi, 3:diff kapa, 4:all diff

clock = 0 * 0:no clock, 1:clock; 2:local clock; 3:CombinedAnalysis
fix_kappa = 0 * 0: estimate kappa; 1: fix kappa at value below; 2: kappa for branches

kappa = 2 * initial or fixed kappa

fix_alpha = 0 * 0: estimate alpha; 1: fix alpha at value below
alpha = 0.5 * initial or fixed alpha, 0:infinity (constant rate)

Malpha = 0

*1: different alpha’s for genes, 0: one alpha*

ncatG = 5# of categories in the dG, AdG, or nparK models of rates

ncatG = 5

nparK = 0 * rate-class models. 1:rK, 2:rK&fK, 3:rK&MK(1/K), 4:rK&MK

nhomo = 2 * 0 & 1: homogeneous, 2: kappa for branches, 3: N1, 4: N2
getSE = 1 * 0: don’t want them, 1: want S.E.s of estimates

RateAncestor = 1 * (0,1,2): rates (alpha>0) or ancestral states

Small_Diff = 7e-6

cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
method = 0 * Optimization method 0: simultaneous; 1: one branch a time

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