Scale Bar in Fig Tree

[Miguel Vizoso]

Dear Andrew,

I performed a maximum likelihood analysis in PAUP. My trees were un-
rooted and I saved the bootstrap and branch lengths values.

When I open the consensustree.nex file with Fig Tree, I can observe a
scale bar. I cannot understand the meaning of this scale bar (e. g.
50.0). Is it important? Is it necessary if I want to publish the
trees? Which meaning should be used in my trees? (e. g. the number of
nucleotide substitutions between the sequences?)

Yours sincerely,

Miguel Vizoso
University of A Coruña, Spain.

[Andrew Rambaut]

The scale bar represents the scale of the branch lengths. I may be wrong
but I would imagine that PAUP is saving the bootstrap values as branch
lengths? It seems likely that the scale bar is meaningless and should be
turned off.

Andrew

[Miguel Vizoso]

Dear Dr. Andrew,

 

thank you very much for your comments, they helped me to solve the problem. I used all the trees generated by PAUP, each one containing branch lengths, and ran the SplitsTree program to obtain the consensus tree with the median branch lengths.

Best wishes,

Miguel.

 

2010/9/16 Andrew Rambaut <ram...@gmail.com>

--
Miguel Vizoso. Universidad de La Coruña.
Grupo de Investigación en Biología Evolutiva
www.udc.es/dep/bm/genetica/gibe