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.
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niuzx9581 •
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.
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.
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.
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