[BioC] APE package on phylogenetic tree plot

[guest [guest]]

Hello R users,

I tried to used both APE and apTreeshape to plot the phylogenetic tree from the generated tree or OTU table. I have the tree file generated from Qiime, but when I use the following command to read the tree, it has the following error message:

> t <- read.nexus("rep_phylo.tre")
Error in start:end : NA/NaN argument

I checked the tree as below:
coveragePerOrigin
     1      2      3      4      5      6      7      8      9     10     11     12     13     14 
 11788  13073  14150  13739  14212  14555  14498  15879  16634  17753  19651  23185  28858 109511 

It seems that the tree is not the format required by APE or something. Any input would be appreciated.

Thanks a lot for the help.



 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] apTreeshape_1.4-5 ape_3.0-11       

loaded via a namespace (and not attached):
[1] grid_3.0.1      lattice_0.20-15 nlme_3.1-110    quantreg_5.05   SparseM_1.03    tools_3.0.1 

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