How to generate a scale for a phylogenetic tree?

[gauravdube]

Dear All,

I have generated phylogenetic trees for a gene dataset by Neighbor joining and Maximum likelihood methods with 1000 boostrap replicates using PHYLIP v3.69 package. I observed in various research articles that the phylogentic trees also have a scale-bar (which mostly represents residue substitution per site). When I visualized the generated trees in FigTree v1.4.2, the scale bar unit (number) seems to be in thousands! While mostly the scale bar represents 0.1 or 0.5 such numbers. Moreover, I visualized the trees in MEGA v6, so as to find out whether FigTree possess any bug or not, but the option for statistics/scale cannot be used therein due to some unknown reasons. I intend to add a scale bar to my tree graphs, please advice me how to generate the optimal scale and value in accordance with the graphs.

Thanks. Gaurav.

P.S: Please let me know if you want to know about the parameters used in NJ and ML methods, if they would help you in providing a solution.

[Roy]

Sounds like you are using consense, which returns "branch lengths" which are in fact the number of bootstrap replicates which support that branch. See:

http://evolution.genetics.washington.edu/phylip/faq.html#wierdtree

https://www.biostars.org/p/9511/