Hi Laura.
I can't comment on FigTree as I have not used it; however you can also
read this format file in R using the phytools function read.simmap.
These trees can then be plotted using plotSimmap in right or left-facing
square phylogram format, which different node placements; or in circular
("fan") phylogram format. There is also a function to add a legend
(add.simmap.legend) and many other helper functions for this modified
"phylo" object class (drop.tip.simmap, reorderSimmap, ladderize.simmap,
etc.).
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org
On 7/7/2015 5:32 PM, Jackson, Laura Marie wrote:
Hi all,
I am trying to visualize my ancestral state reconstruction created in Mesquite
(exported as a SIMMAP 1.5 format) in Figtree. In the Mesquite manual it said this is
possible (see below). However, I am not able to see any branch mapping on the tree
file after opening in Figtree. I tried selecting �colour by" and map* under the
Appearance tab, but still no mapping. If this is not possible in Figtree, do you
have any suggestions for tree visualization from Mesquite to another program? I have
a large tree, and Mesquite does not have many options for visualization editing. Any
help with this would be greatly appreciated!
* You can now export ancestral state reconstructions to a tree description with embedded
ancestral states in the format of SIMMAP<http://www.simmap.com/> 1.5, which can then be
subsequently read by FigTree<http://tree.bio.ed.ac.uk/software/figtree>. To do this,
have the ancestral states recontructed in a Tree window using Trace Character History. Then,
in the Trace menu, choose Export Ancestral States Trace>SIMMAP 1.5 Format. The tree file
saved can be read by FigTree.
-Laura
---
Laura M. Jackson
PhD Student
Department of Biology
185 Churchill Haines
University of South Dakota
414 E. Clark St.
Vermillion SD 57069-1746
Email: [email protected]<mailto:[email protected]>
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