Hi everyone,
I am running yn00 to analyze around 35000 alignments. My codon alignments were generated by pal2nal in PAML input format. When I run the yn00, dn,ds is calculated only for around 300 alignments but not for the rest ~34000 alignments. I tried running these alignments one by one and I get the same error for all of them.
Error in sequence data file: E at 3 seq 1.
Make sure to separate the sequence from its name by 2 or more spaces
I have checked my alignments and they seem to be fine, as in , in multiples of three. It's very confusing as ~200 of them seem to not have this problem although they were all generated by pal2nal. I am attaching a few alignments that did not run. Please help me figure this out. Thank you.
2 642
ENSMUSG00000004821_ENSMUST00000004943_Tmed11_5_108777235_108795363
ATGCAAATTCAGACAATTCTTTTATGTTTTAGCTTTTCATTTTCAGCTGCTTTTTATTTC
CATGCTGGAGAGCGAGAGGAGAAATGTATAATTGAAGACATTCCAAGTGATACATTGATA
ACAGGGACATTCAAGGTACAGCAGTGGGACATAGTCAGACATGACTTCCTTGAATCTGCT
CCTGGCTTAGGAATGTTTGTGACTGTTACAACTAATGATGAGGTATTATTATCCAAGTTA
TATGGTGCACAAGGAACATTCTATTTTACTTCTCATTCATCTGGTGAACACATCATTTGC
TTAGAATCTAATTCTACACAGTTTGTGTCATTTGGAGGAAGTAAGCTGCGCATCCACTTA
GATATTCGAGTTGGAGAACATGACCTTGATGCAGCTATTGTTCAAGCAAAGGATAAAGTT
AATGAAGTAACCTTCAAGCTTCAACATCTAATTGAACAAGTGGAGCAAATACTCAAAGAA
CAAGACTATCAAAGGGACCGTGAAGAAAATTTCCGTATAACCAGTGAAGATACCAATAGA
AATGTTTTATGGTGGGCTTTTGCACAAATATTGATCTTTATCTCAGTTGGAATTTTTCAA
ATGAAACACCTTAAAGATTTCTTCATAGCTAAGAAGCTTGTT
ENSRNOG00000000035_Tmed11_ENSRNOT00000000040_14_1932659_1953305
ATGCAAACTCAGACAATTCTCTTATGTTTCAGTTTTTCCTTTTCAGCTGCTTTTTATTTC
CATGCTGGGGAGCGAGAGGAGAAATGTATAATCGAAGACATTCCAAGTGACACGTTGATA
ACAGGGACATTCAAGATACAGCAGTGGGACATTGGTAGACATGACTTTCTTGAATCTGCT
CCTGGCTTAGGAATGTTTGTGACTGTTACAAACAATGATGAGGTATTATTATCCAAGTTA
TATGGTGCACAAGGGACATTCTATTTTACTTCACACTCATCTGGTGAACACATCATTTGC
TTAGAATCTAATTCTACACAATTTGTGTCATTTGGAGGGAGTAAGCTGCGCATCCACTTA
GATATTCGAGTTGGAGAGCATGACCTTGATGCAGTTATTGTTCAAGCAAAGGACAAAGTT
AATGAAGTAGCCTTCACGCTTCGACATCTAATTGAACAAATTGAACAAATACTCAAAGAA
CAAGACTATCAAAGGGACCGTGAGGAAAATTTCCGTATCACCAGTGAAGATACCAATAGA
AATGTTTTATGGTGGGCTTTCGCACAAATATTAATCTTTATCTCAGTTGGAATTTTTCAA
ATGAAGCACCTTAAAGATTTCTTCATAGCTAAGAAGCTTGTT
Sorry for this format.I couldn't figure out how to attach a file here.