"ProtTest: wrong tree format, exiting..." when running ProtTest

Question

[niuzx9581]

Hi!

First I obtained 295 single copy orthologues from 36 bacterium CDS file through orthofinder. Then I want to use that data to construct phylogenetic tree. However, when I concatenated these single copy gene to one .fasta file and find best fit model in ProtTest, the error "ProtTest: wrong tree format, exiting..." still exit. Some one in Github said "PhyML cannot handle such a big alignment. If I'm not wrong, there are 2 constraints for the alignment size in PhyML: There is a limit of 4,000 taxa, and NTAXA * NTAXA * SEQLEN should not be greater than 10^8. I'm sorry about that."

Even if I reduced my input sequence number to 15, which is smaller than 10^8, it still doesn't work. So I want to know how to solve these problem.

Answer 1

[Mensur Dlakic]

the error "ProtTest: wrong tree format, exiting..." still exit

The error clearly has to do with file format, not alignment size. I think it expects the alignment in Phylip format, with sequence names not longer than 10 characters. You will also have to be sure that the names are unique.

[niuzx9581]

Thank you very much! I changed my file name less than 10 characters and the software goes well! But I have another question that how long does ProtTest usually run? It has been running for 24 hours but has not yet completed.

[Mensur Dlakic]

That sounds like a big alignment, and I have no idea how many CPUs you have and whether all of them are being used. But yes, it has been known to take several hours up to half a day for smaller alignments than yours.

IQ-TREE has a mode called ModelFinder that can probably do the same task faster than ProtTest3, especially if you have a computer with many CPUs.