Question: Bootstrapping In Clustalw
gravatar for raunakms
8.8 years ago by
San Francisco
raunakms1.1k wrote:

I've a set of nucleotide sequences and I used clustalw v.2.1 to align those sequences. The next thing I did was to generate a tree using the .dnd file in a Tree visualization software. I incorporated a -BOOTSTRAP function in the clustalw but the tree did not display the bootstrap value. I even checked the .dnd file with only listed the distance value but not the bootstrap value.

The command I used in the perl script for clustalw alignment was

system("$clustalw -INFILE=$in_file  -OUTFILE=$out_file -TYPE=DNA -CLUSTERING=NJ -BOOTSTRAP=1000 -CONVERT=Phylip");

How can I display the bootstrap values in the tree? Is anything missing in my command? I did not get a clear explanation on it in the clustaw help file!!

clustalw tree • 5.9k views
ADD COMMENTlink modified 8.7 years ago by Gustavo530 • written 8.8 years ago by raunakms1.1k

What software are you using to view the tree? There may be an option to show/hide the bootstrap values, or to place them at nodes/leaves.

ADD REPLYlink written 8.8 years ago by Neilfws49k

I'm using FigTree ( to visualize the Tree. There is an option in FigTree to display branch length or its values. But the original .dnd file itself does not contain any bootstrap values !!!

ADD REPLYlink written 8.8 years ago by raunakms1.1k
gravatar for Gustavo
8.8 years ago by
Gustavo530 wrote:

The .dnd file isn't a phylogenetic tree (even though it has a similar format): it is a "guide tree" for the alignment stage.

When you use the clustalw option to create a phylogenetic tree with bootstrap, select phylip output format. The bootstrap values will be included in the phylip output.

(Edited to add: I see you already indicated phylip output. See if the run produced a separate .phy file for this, not the .dnd file.)

ADD COMMENTlink written 8.8 years ago by Gustavo530
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