Related to the multiple bootstrap values emitted with -bb/-B and -alrt discussed in https://github.com/iqtree/iqtree2/discussions/249 - I am getting multiple bootstrap values despite only specifying -bb.
Originally posted by **finwe858** June 27, 2024
> Hi,
> I run a ML analyses on the IQ web server with the next command line:
> `../../iqtree -s cyt-134-haploonly+corrected.fas -st DNA -m HKY+I+G4+F -bb 1000 -alrt 1000`
> In the output trees both balues are provided with a /, but I cannot find what value stands for what analyses. I assumed that UB should be the first number (as it is first in the command line)? In my output most values before '/' are lower than after it. 97.2/100, 43.1/89, 73.3/96 as few exmples
> In the FAQ it is recommended to: One would typically start to rely on the clade if its SH-aLRT >= 80% and UFboot >= 95%.
> So, still confused what values stand for the UB and which for SH.
> Thanks
My question is as follows:
Please forgive my relative ignorance here, but I have a treefile from a -bb 1000 bootstrapping run, and there are two values for each node, separated by a forward slash exactly as the example in the referenced query (#249). However, I didn't add the -alrt flag to the command line, and my iqtree file has the statement that Numbers in parentheses are ultrafast bootstrap support (%), with no mention of aLRT. The ASCII tree also has two values in the parentheses by each node, e.g. (77/96) or (100/75). Most are (smaller/bigger) but not all. I imagine there is some significance to the tree being unrooted and the value beside the most basal branch having only a single value (62).
As a result, the treefile doesn't open in FigTree...
My CL was as follows:
iqtree2 --polytomy -djc -s <aln file> -m GTR+R6 -pre C105 -t <guide tree file> -bb 1000 -nm 100000 -nstop 500 -T 15
The large -nm 100000 resulted from a failure to converge with smaller values - I can't see how to force iqtree to continue until convergence is achieved as well as -nstop 500 for example, but that's another issue entirely!
Related to the multiple bootstrap values emitted with
-bb/-Band-alrtdiscussed in https://github.com/iqtree/iqtree2/discussions/249 - I am getting multiple bootstrap values despite only specifying-bb.My question is as follows:
Please forgive my relative ignorance here, but I have a treefile from a
-bb 1000bootstrapping run, and there are two values for each node, separated by a forward slash exactly as the example in the referenced query (#249). However, I didn't add the-alrtflag to the command line, and my iqtree file has the statement thatNumbers in parentheses are ultrafast bootstrap support (%), with no mention of aLRT. The ASCII tree also has two values in the parentheses by each node, e.g.(77/96)or(100/75). Most are(smaller/bigger)but not all. I imagine there is some significance to the tree being unrooted and the value beside the most basal branch having only a single value (62). As a result, the treefile doesn't open in FigTree...My CL was as follows:
iqtree2 --polytomy -djc -s <aln file> -m GTR+R6 -pre C105 -t <guide tree file> -bb 1000 -nm 100000 -nstop 500 -T 15The large-nm 100000resulted from a failure to converge with smaller values - I can't see how to force iqtree to continue until convergence is achieved as well as-nstop 500for example, but that's another issue entirely!Many thanks for any help