Bootstraps values in iqtree

Question

[Begonia_pavonina]

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?

Answer 1

[patrickdm]

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.

[Begonia_pavonina]

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