Can anyone suggest a program/ software which helps to remove the bootstrap values from the phylogenetic tree file?
Maybe you can try using the ape package in R?
install.packages("ape") # Install ape package if you don't have it already
library(ape) # Load the ape package
setwd("path/to/your/tree") # Put here the directory where your tree is
tree
Thanks Artur for the reply.
FigTree is my favorite too. But it is a graphical viewer for viewing the phylogenetic trees. My need here is a tree file in Newick format, which is void of bootstrap information in it. Repeating the analysis is also not a feasible task as it is a big data set and it takes more than a week's time in a cluster computer to complete the run.
Use MEGA 6.0 programme for phylogenetic analysis. There you have option for with or without bootstrap value or you can remove the bootstrap value.
My favorite program, Seaview, was designed by French colleagues...
If you don't want to rerun the analyse, you can always remove the bootstrap values in your tree files using the egrep function or in your figure file using an image editors...
There are plenty of tricks when it comes to communicate about phylogenetic results.
Line
If you decide to run again the analysis, you can use DARwin6 software. You can find it using google and it is free. You have many options. You can add bootstrap values of not. You can also use different colors for your populations or sub populations...
you can save the tree as pdf format, then using the Illustrator to remove the value. Or just use the Figtre
Maybe you can try using the ape package in R?
install.packages("ape") # Install ape package if you don't have it already
library(ape) # Load the ape package
setwd("path/to/your/tree") # Put here the directory where your tree is
tree
Maybe you can try using Treeview program for viewing the tree. There you have option for with or without bootstrap value.
Thank you all for your inputs. It was very useful. I have tried in FigTree as well as used R. It helped me to solve my issue.
Thanks..
I think the easiest and fastest way to do it would be to load the newick file in Vim and run the following command:
%s/)\d\*/)/g
Save (or save as) the file and your are done.
Hope it helps.
Dear Sunitha,
What program did you use to generate the phylogenetic tree?
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