Hi,
I am getting an error using dist.multiPhylo of package distory that I am
unable to decipher.
I wish to compute the geodesic distance between 2 trees (t1 and t2) in
nexus format (see copy below).
I combine them in a list:
L <- list(t1, t2) # then I invoke the function:
dist.multiPhylo(L) #and get the following error:
Error in dist.multiPhylo(x, method = method, force.multi2di =
force.multi2di, :
An error was encountered in parsing near position 39: Couldn't figure
out what to do after a second leaf entry
Any idea, help will be very much appreciated.
Juan
******************************************************************
THE TREES:
t1:
#NEXUS
[R-package APE, Fri Mar 22 16:37:39 2019]
BEGIN TAXA;
DIMENSIONS NTAX = 9;
TAXLABELS
Mugliz
Mcepha1
Chesub
Lizahaem
Lizaram
Chelab
Lizaaur
Lizasal
Valabuc
;
END;
BEGIN TREES;
TRANSLATE
1 Mugliz,
2 Mcepha1,
3 Chesub,
4 Lizahaem,
5 Lizaram,
6 Chelab,
7 Lizaaur,
8 Lizasal,
9 Valabuc
;
TREE * UNTITLED = [&R]
((1:0.00826986,2:0.02165651)985:0.3174293,(((3:0.08488147,4:0.09383585)969:0.02111665,(5:0.0488584,((6:0.03890206,7:0.03355451)545:0.00550473,8:0.04896926)594:0.01171567)930:0.02600083)545:0.06207831,9:0.13004227)321:0.00534938)195;
END;
***********************************************************
t2:
#NEXUS
[R-package APE, Fri Mar 22 16:37:57 2019]
BEGIN TAXA;
DIMENSIONS NTAX = 9;
TAXLABELS
Valabuc
Chesub
Lizasal
Lizahaem
Mugliz
Mcepha1
Lizaaur
Chelab
Lizaram
;
END;
BEGIN TREES;
TRANSLATE
1 Valabuc,
2 Chesub,
3 Lizasal,
4 Lizahaem,
5 Mugliz,
6 Mcepha1,
7 Lizaaur,
8 Chelab,
9 Lizaram
;
TREE * UNTITLED = [&R]
(1:0.44662136,(2:0.18111073,((3:0.06637225,(4:0.02497353,(5:0.04256194,6:0.03313771)561:0.00410113)966:0.06080073)909:0.05298036,(7:0.05777136,(8:0.03691804,9:0.04690791)1000:0.04129831)602:0.01447255)918:0.07520298)706:0.11656507)1000;
END;
--
Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
Symbiont Ecology and Evolution Lab
University of Valencia http://www.uv.es/~balbuena
<http://www.uv.es/%7Ebalbuena>
P.O. Box 22085 http://www.uv.es/cophylpaco
<http://www.uv.es/cavanilles/zoomarin/index.htm>
46071 Valencia, Spain
e-mail: j.a.balbu...@uv.es <mailto:j.a.balbu...@uv.es>tel. +34 963 543
658 fax +34 963 543 733
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
*NOTE!*For shipments by EXPRESS COURIER use the following street address:
C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain.
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