I try to output bootstraps values with iqtree in the Newick format with the following code:
iqtree -s file.phy \
-nt AUTO \
-m PMB+F+R2 \
-B 1000
According to the documentation, the bootstraps support values are added to the outputs with the flag -B. However, they are not added to the .treefile output, but given in a separate file .splits.nex, which cannot be used to drawn a phylogenetic tree.
Would anyone know how to get the bootstraps values in the .treefile, like in the Rich Newick format?
Hello, is it possible that you are referring to the iqtree2 docs, while using the iqtree program?
I can find the -B option in iqtree2 -h,
ULTRAFAST BOOTSTRAP/JACKKNIFE:
-B, --ufboot NUM Replicates for ultrafast bootstrap (>=1000)
but not in iqtree -h, where boostraps flags are
ULTRAFAST BOOTSTRAP:
-bb <#replicates> Ultrafast bootstrap (>=1000)
-bsam GENE|GENESITE Resample GENE or GENE+SITE for partition (default: SITE)
-wbt Write bootstrap trees to .ufboot file (default: none)
-wbtl Like -wbt but also writing branch lengths
-nm <#iterations> Maximum number of iterations (default: 1000)
-nstep <#iterations> #Iterations for UFBoot stopping rule (default: 100)
-bcor <min_corr> Minimum correlation coefficient (default: 0.99)
-beps <epsilon> RELL epsilon to break tie (default: 0.5)
-bnni Optimize UFBoot trees by NNI on bootstrap alignment
-j <jackknife> Proportion of sites for jackknife (default: NONE)
STANDARD NON-PARAMETRIC BOOTSTRAP:
-b <#replicates> Bootstrap + ML tree + consensus tree (>=100)
-bc <#replicates> Bootstrap + consensus tree
-bo <#replicates> Bootstrap only
hth.
Thank you patrickdm, it was indeed the wrong flag for the wrong software.
I have eventually used the single branch test assesment with the following command:
iqtree -s file.phy \
-nt AUTO \
-m PMB+F+R2 \
-alrt 1000
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