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Abnormal reading of FASTA file by PAL2NAL

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  • Abnormal reading of FASTA file by PAL2NAL

    I am making a script that produces as an output a protein alignment in fasta format and an appropriate mRNA fasta file for latter use with the PAL2NAL algorithm that gives a codon aware alignment.

    PAL2NAL is reading the mRNA fasta file normally, the same cannot be said for the protein file. This is the error that the web based interface gives:

    ERROR: number of input seqs differ (aa: 82; nuc: 43)!!

    It is reading the fasta file as if it has 82 sequences, when it really has the same amount as the mRNA fasta file. I've never had this problem before, what am I missing? Thank you for the help . Attached are both files. Protein alignment mRNA file