Where are the bootstrap values in RAxML trees?

[liuyuwen1]

Dear developers,
From other's issue I saw that you have said The .tre output is the one generated by FastTree as is the first tree built by PhyloPhlAn (I'm assuming your config file contains both sections [tree1] and [tree2], with FastTree specified in [tree1] and RAxML in [tree2]). So the final phylogeny you should consider is the RAxML_bestTree_....
And here are my configuration file script

phylophlan_write_config_file \
-o bartonella2_config.cfg \
-d a \
--force_nucleotides \
--db_aa diamond \
--map_aa diamond \
--map_dna diamond \
--msa mafft \
--trim trimal \
--tree1 fasttree \
--tree2 raxml

In my output file, I can find bartonella.tre, bartonella_resolved.tre, RAxML_bestTree.bartonella_refined.tre, RAxML_info.bartonella_refined.tre, RAxML_log.bartonella_refined.tre, RAxML_result.bartonella_refined.tree. And I know that the final phylogeny I should consider is the RAxML_bestTree.bartonella_refined.tre.

But I have noticed that there aren't bootstrap values in RAxML_bestTree.bartonella_refined.tre. while bartonella.treand bartonella_resolved.tre have. And I need to show the bootstrap values in my final tree. I don't know that if there are bootstrap values in the RAxML tree and Where can I find the bootstrap values ?

Many thanks for your help,
Best regards,
Liu yuwen

[Sidduppal]

PhyloPhlan does not generate bootstrap values by itself, you'll have to use the alignment file generated by PhyPhlan to create your tree with bootstrap values. An example command might be:
raxmlHPC-PTHREADS-SSE3 -s <your alignment file> -n <your output file> -f a -m PROTCATLG -# 100 -p 1989 -x 1989 -T 20
You can also specify these parameters in the config file.

[acvill]

I came across this thread while trying to add bootstrap annotations onto the RAxML_bestTree file generated as part of the StrainPhlAn workflow. After specifying -f a to perform a rapid bootstrap analysis using the existing alignments, you need to then run RAxML again with ­-f b to append the bipartition information onto the tree. An example workflow:

raxmlHPC-PTHREADS-SSE3 -s ${strain}.StrainPhlAn4_concatenated.aln -n bs100 -f a -m PROTCATLG -# 100 -p 1989 -x 1989 -T 20  
raxmlHPC-PTHREADS-SSE3 -f b -t RAxML_bestTree.${strain}.StrainPhlAn4.tre -z RAxML_bootstrap.bs100 -m PROTCATLG -n BestBoot

The tree with bootstrap values at node labels can then be read and visualized in R.

library(treeio)
library(ggtree)
treeb <- read.raxml(file = "RAxML_bipartitionsBranchLabels.BestBoot")
ggtree(treeb, layout = 'rectangular') +
  geom_tiplab(mapping = aes(label = label)) +
  geom_nodelab(mapping = aes(label = bootstrap))

I realize that there's probably a way to generate a tree with bootstrap annotations as part of the strainphlan run by modifying the default configs and specifying --phylophlan_configuration when strainphlan is called. But I couldn't edit the configs without creating errors. It would be great if the maintainers could provide a working config file to use as part of phylophlan/strainphlan workflows to create bootstrapped RAxML trees.