Alastair,
That's indeed the correct work-around. The is because a different code
is used whether the NEXUS file has a TRANSLATE block or not. I'll fix
the bug very soon.
Cheers,
Emmanuel
PS: thanks for the tip on using Figtree.
Alastair Potts wrote on 24/02/2011 14:57:
Hi All,
I think I have located the problem. As usual I had experienced it before
and I found (or someone else found) a workaround - but I couldn't
remember it.
The bootstrap values ($node.label) is mixed up when I save the bootstrap
tree as a nexus file with a translation table in PAUP (this is the
default by the way). If I save the bootstrap tree without a translation
table (i.e. FORMAT=ALTNEX), then the BS values are in their correct places.
If I open both saved bootstrap trees (i.e. with and without translation
tables) in FigTree, I get identical trees with the bootstrap labels in
the correct places. Obviously this has not been the case in R. I think
that there may be a problem when reading in the translation table when
there are values included with each node. I've included examples of both
saved files from PAUP if anyone wishes to play around with the problem.
So, for those of you using PAUP, the quick work-around to avoid this
problem in future is to use SAVETREES ... FORMAT=ALTNEX ...
Cheers,
Alastair
-----------------------------------------------------------------
Alastair Potts
PhD candidate
Botany Department
University of Cape Town
alastair.po...@uct.ac.za or pott...@gmail.com
University Private Bag, Rondebosch 7700, South Africa
or
PO Box 115, Loxton 6985, South Africa
Cell: 082 491-7275
-----------------------------------------------------------------
Emmanuel Paradis wrote:
Hi Alastair,
I copied the Newick string below into R, read it with read.tree, and
this seems to work as normal.
I also tried to do the same with Figtree: the tree and its tip labels
are OK, but the node labels are not (eg, it displays "377" for the
root instead of "100"). My guess is that it's a problem when decoding
the strings (maybe specific to Linux).
Best,
Emmanuel
Alastair Potts wrote on 23/02/2011 21:09:
Hi All,
I'm sure I've had this problem before and found a way to fix it. I've
spent an hour looking for the solution, but can't seem to find it.
In short, I've run a bootstrap analysis in PAUP* which provided a
consensus tree with bootstrap values. This tree opens fine in
FigTree. I read it in using ape's read.nexus and plot the node using
nodelabel and the $node.label property of the imported tree. I've
done nothing else to the tree (e.g. ladderize which I know sometimes
causes problems), yet my node label bootstrap values are all shuffled
around in some way and I can't figure out why.
My code is simply:
pt <- read.nexus('dataset1.bootstrap.swap.NNI.tree')
plot(pt,cex=0.7)
nodelabels(pt$node.label)
Possibly the problem lies with the nexus tree, so here it is for what
it's worth:
tree PAUP_1 = [&U]
(1:0,((2:100,(3:100,4:100)80:80,5:100,6:100,(7:100,10:100)60:60,8:100,9:100,(11:100,34:100)60:60,15:100,(16:100,37:100,54:100,56:100,57:100,71:100,72:100)70:70,18:100,(23:100,25:100,30:100,31:100,35:100,116:100,117:100)59:59,26:100,27:100,32:100,33:100,39:100,48:100,58:100,59:100,60:100,64:100,69:100,70:100,78:100,79:100,80:100,82:100,(83:100,84:100,85:100)52:52,94:100,99:100,101:100,102:100,107:100,119:100)70:70,(12:100,(13:100,14:100,53:100,90:100)69:69,28:100,(62:100,63:100)96:96,(66:100,67:100)69:69,68:100,91:100,92:100,93:100,97:100,98:100,100:100)81:81,(17:100,19:100,21:100,24:100,38:100,42:100,43:100,(44:100,45:100)67:67,47:100,49:100,50:100,61:100)82:82,(20:100,40:100,41:100,51:100,52:100,73:100,74:100,108:100,109:100,110:100,118:100)65:65,(22:100,29:100,36:100,46:100,75:100,76:100,105:100,111:100,112:100,113:100,114:100,115:100)97:97,55:100,(65:100,86:100,89:100,96:100)68:68,(77:100,(81:100,95:100,103:100,104:100)68:68,106:100)65:65,(87:100,88:100)98:98)100:100)1
00
;
My apologies for not setting up a standard replication of the error -
but I'm not really sure how to go about it with this example.
Thanks in advance for your help.
Cheers,
Alastair
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Emmanuel Paradis
IRD, Jakarta, Indonesia
http://ape.mpl.ird.fr/
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