Error code for .phy file

[ek...@cornell.edu]

ERROR    | 2016-02-25 00:41:23,159 | Error in Alignment Parsing:Expected W:(0123...) (at char 0), (line:1, col:1)

ERROR    | 2016-02-25 00:41:23,159 | A common cause of this error is having whitespace, i.e. spaces or tabs, in the species names. Please check this and remove all whitespace from species names, or replace them with e.g. underscores

I removed spaces and replaced them with underscores, this problem seems to persist 

[Rob Lanfear]

Hi,

The fact that you had spaces in your species names suggests that you might not have read the manual. The manual specifies exactly how to format your phylip file so that it will work on page 11, as well as ways that you can make sure your file is in the right format:

The phylip format: Your alignment needs to be in Phylip format. We use the same
version of Phylip format that PhyML uses, which is described in detail here
http://www.atgc-montpellier.fr/phyml/usersguide.php?type=phylip. In brief, this format
should contain a line at the top with the number of sequences, followed by the number
of sites in the alignment. After that, there should be one sequence on each line, where a
sequence contains a name, followed by some whitespace (either spaces or tabs) and the
sequence. Names can be up to 100 characters long. There should be nothing else on
the line other than the name and the sequence – watch out if you use MacClade, which
adds some extra things to the end of each line.

Converting other formats to phylip: If you have an alignment in some other format and
want to convert it into phylip format, the best (free!) tool to use is Geneious. Other
alignment editors tend to cut the names short in phylip files (the original definition had
a 10 character limit on names), but Geneious doesn’t. If you don't have Geneious, it's
free and you can download it from http://www.geneious.com/. Once you have
Geneious, follow these steps to convert your alignment file to phylip:

1. Open up your alignment file in Geneious, and highlight it
2. Go the 'File' menu and click 'Export', then 'Selected documents...'
3. Scroll down the list of options and choose 'Phylip (*.phy)', and click 'OK'.
4. Now a box of options will come up, choose 'Export full length'.
5. Save the phylip alignment file in the same folder as your .cfg file for PartitionFinder.

​

If you have followed these instructions, and are still having trouble, please post your alignment (or a section of it) here (or to me off list if you prefer), so that we can figure out the problem and help. Without seeing the alignment, it's impossible to know the issue.

Yours,

Rob

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Rob Lanfear
School of Biological Sciences,
Macquarie University,

Sydney

phone: +61 (0)2 9850 8204

www.robertlanfear.com