How to generate a scale for a phylogenetic tree?

gauravdube · 09-16-2015, 01:56 AM

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 · 09-17-2015, 07:35 AM

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...html#wierdtree
https://www.biostars.org/p/9511/

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09-16-2015, 01:56 AM	#1
gauravdube Junior Member Location: India Join Date: Feb 2014 Posts: 7	How to generate a scale for a phylogenetic tree? 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.

09-17-2015, 07:35 AM	#2
Roy Member Location: Sheffield, UK Join Date: Oct 2009 Posts: 17	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...html#wierdtree https://www.biostars.org/p/9511/