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Revert "Simplify multifurcation resolution in the stepwise inference tutorial" #147

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Merged
davidcerny merged 1 commit into from
Apr 27, 2026
+7 −3
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Revert "Simplify multifurcation resolution in the stepwise inference tutorial" #147

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4 changes: 3 additions & 1 deletion tutorials/sequential_bayes/scripts/mcmc_ultrametric.Rev
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Expand Up @@ -93,7 +93,9 @@ time_tree ~ dnBirthDeath(rootAge=root_time, lambda=birth_rate, mu=death_rate, ta
unrooted_MAP_tree = readBranchLengthTrees("output/photinus_"+GENE+"_MAP.tre")[1]

## resolve the trifurcation at the root
unrooted_MAP_tree.resolveMultifurcations(resolveRoot=TRUE)
root_index = 2*unrooted_MAP_tree.ntips() - 2
first_child = unrooted_MAP_tree.getDescendantTaxa( unrooted_MAP_tree.child( root_index, 1 ) )
unrooted_MAP_tree.reroot( clade(first_child), makeBifurcating=TRUE)

## make the tree ultrametric and restore node indices
ultrametric_MAP_tree = unrooted_MAP_tree.makeUltrametric()
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6 changes: 4 additions & 2 deletions tutorials/sequential_bayes/stepwise_dating.md
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Expand Up @@ -132,9 +132,11 @@ You could also use an externally rooted tree, which might be preferred.
unrooted_MAP_tree = readBranchLengthTrees("output/photinus_COI_MAP.tre")[1]
```
Since the tree comes from a non-clock analysis, it is unrooted, which is to say it has a trifurcation at the root.
We want to make its root bifurcating, but it is not important to us exactly how we do it, so we will just resolve the trifurcation randomly:
We want to make its root bifurcating, but it is not important to us exactly how we do it. Therefore, we will just grab the first of the three children of the root node and make it the outgroup:
```
unrooted_MAP_tree.resolveMultifurcations(resolveRoot=TRUE)
root_index = 2*unrooted_MAP_tree.ntips() - 2
first_child = unrooted_MAP_tree.getDescendantTaxa( unrooted_MAP_tree.child( root_index, 1 ) )
unrooted_MAP_tree.reroot( clade(first_child), makeBifurcating=TRUE)
```
We also need to make the tree ultrametric:
```
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