[phylocom-user] Phylocom input files

Steven Kembel steve.kembel at gmail.com
Thu May 20 15:25:37 PDT 2010

Hi Seara,

Your phylogeny has scientific notation for some of the really short branch lengths (i.e. "1.44515208833423E-6"). Phylocom doesn't deal well with non-numeric characters in branch lengths. I'd suggest either collapsing very short branches to polytomies or reformatting the branch lengths. You can do this in R using the ape package function di2multi (to collapse short branches to polytomies). And the write.tree function in ape allows you to specific the number of digits used for printing branch lengths. Read your tree into R with read.tree, collapse the polytomies if you want, write it out again with write.tree and the digits parameter set to a value that gets rid of the non-numeric characters in your branch lengths.

Your sample file needs to be sorted by sample name. Please have a look at the Phylocom manual for a detailed explanation of how the sample file should be formatted.

The branch length issue is coming up a lot lately, I will add the solution above to the manual in future versions. For others having trouble loading files into Phylocom, a troubleshooting tip is to first try loading just the phylogeny. You could do this by typing "phylocom phydist -f phyloFileName", since this function loads just the phylogeny. If this fails, there is a problem with your tree. Often branch length formatting is the issue if the tree otherwise appears to be a valid Newick string. If phydist works but comstruct or other functions do not work, the problem is with your sample or traits file. There are a few functions in the picante package for R (writesample, writetraits) that can be used to easily generate properly formatted sample and traits files for use by Phylocom.


On May 19, 2010, at 9:25 PM, Lim wrote:

> Hi,
> I'd greatly appreciate if someone can help me figure out what's wrong
> with my input files!
> The sample data is in txt format (attached), and the final line has a
> return character.  The newick tree file has a semicolon at the end,
> and the taxa names do not begin with a number.  However, I'm getting
> the error message:
> File `likelihood.txt' has unix newlines
> Bus error
> Thanks!
> Seara Lim
> MSc student
> University of British Columbia
> <likelihood.txt><likelihood.nwk>_______________________________________________
> phylocom-user mailing list
> phylocom-user at lists.phylodiversity.net
> http://lists.phylodiversity.net/listinfo.cgi/phylocom-user-phylodiversity.net

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