Question: Raxml (Residues Read In Sequence)
0
gravatar for Gabriel R.
5.1 years ago by
Gabriel R.2.6k
Center for Geogenetik Københavns Universitet
Gabriel R.2.6k wrote:

I am running RAxML version 7.3.2 on a file in phylip format. I check manually and all my lines have an equal amount of characters. When I run raxml, I get:

50 (instead of 40) residues read in sequence 9 [ID here]

But my sequences are DNA and are much longer than 50. Am I missing anything obvious here ?

• 1.3k views
ADD COMMENTlink modified 5.0 years ago by Biostar ♦♦ 20 • written 5.1 years ago by Gabriel R.2.6k

Not easy to give an answer without seeing the file. Which phylip format is it? Interleaved or sequential? How did you generate the phylip alignment?

ADD REPLYlink written 5.1 years ago by Joseph Hughes2.7k

interleaved and it was generated using seqret from a fasta alignment.

ADD REPLYlink written 5.1 years ago by Gabriel R.2.6k

Raxml is quite relaxed about file format but it is most likely something to do with the format or the EOF. Can you show you top 12 lines?

ADD REPLYlink written 5.1 years ago by Joseph Hughes2.7k
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