[phylocom-user] AOT segmentation fault

Anthony Amend amend at hawaii.edu
Fri Mar 23 08:53:43 PDT 2012

Hi Phylocom community,

Sorry for the bother, but I am at my wit's end.

Like the last poster, I've been analyzing my data in Picante, but am interested in working with the AOT functions in phylocom.  Converting my files was a bit of work, but I renamed all of my integer taxon IDS (by prepending QQQ) and named all of my nodes (node1,node2 etc.).

When I try to use aotf in phylocom (4.1) on my mac OS 10.6.8 using the following commands:

phylocom aotf  -s phylo.comm -f pruned_phylo.tree  -t phylo_traits > aot_out
I get an error reading:

File 'phylo_traits' has mac newlines
Segmentation fault
and the output is blank

Changing my newlines to Unix doesn't help things, I just get a different flag.

Interestingly, these same files work for other phylocom functions, like comdist.

I thought that something may be odd with my tree file, so I created versions without node values and without branch lengths (or node values).  But these trees produce the following error:

Abort trap

I've gone through the help forum, but I don't see that anyone else has had this problem.  Any ideas?

My files are posted here:


Thanks in advance for any advice!


Irvine, CA 92697


amend at hawaii.edu

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