Open RvV1979 opened 6 years ago
Hi RvV1979,
The error happens because ModelTest ignores the '*' (star) character, which occurs once in each sequence except in the second one (i.e., [Seq 1] given that first one is [Seq 0]). Therefore, it counts one fewer character for every sequence (1005) while for Seq1 it counts 1006.
Is there any particular reason for using that character?
Best, Diego.
Hi Diego,
Thanks for the clarifications. The star stands for the stop codon (translation of AUG). They are quite common in protein alignments so it would be great if modeltest could accommodate them appropriately.
Best, Robin
On Tue, Feb 6, 2018 at 6:46 PM ddarriba notifications@github.com wrote:
Hi RvV1979,
The error happens because ModelTest ignores the '*' (star) character, which occurs once in each sequence except in the second one (i.e., [Seq 1] given that first one is [Seq 0]). Therefore, it counts one fewer character for every sequence (1005) while for Seq1 it counts 1006.
Is there any particular reason for using that character?
Best, Diego.
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You're right, thanks!
Actually I figured out that libpll supports '*' character in amino acid sequences, but it is stripped out in fasta parser. Nonetheless, in our analyses it is treated as a gap/missing chararcter, so it could be also replaced by '-' or '?'.
I fixed that.
Hi Diego,
I am testing modeltest-ng on some of my aa alignments in fasta format and so far I always get an "Cannot parse the msa: Wrong sites read" error. For example
$modeltest-ng -d aa -i ../Alignments/OG0010000.fa -T raxml -p 6
produces
What may be going wrong here?
Thanks
OG0010000.fa: