Raxml (Residues Read In Sequence)

Question

[Gabriel R.]

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 ?

[Joseph Hughes]

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?

[Gabriel R.]

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

[Joseph Hughes]

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?