countends doesn't seem to work

mothur bugs
1

The countends=F option doesn’t seem to work with dist.seqs

I take the file test_countendsT.fa which contains:

Id_1
AGCCTAAGCTACAAGCCCTGGAAACGGGGTCTAATACCGGATACGACCTCCGACCGCATGGTCTGGTGGTGGAAAGCTCC
GGCGGTGAAGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCT
GAGAGGGAGCTTAGGCTCTGAGCGGGCTGGCAAGGC
Id_1_endgap
AGCCTAAGCTACAAGCCCTGGAAACGGGGTCTAATACCGGATACGACCTCCGACCGCATGGTCTGGTGGTGGAAAGCTCC
GGCGGTGAAGGATGAGCCCGCGGCCTATCAGCTTGTTGGTGGGGTGATGGCCTACCAAGGCGACGACGGGTAGCCGGCCT
GAGAGGGAGCTTAGGCTCTGAGC-------------

and get the same distance with countends set to T or F:

mothur > system(cp test_countendsT.fa test_countendsF.fa)

mothur > dist.seqs(fasta=test_countendsT.fa, countends=T)
0 0
1 0

mothur > dist.seqs(fasta=test_countendsF.fa, countends=F)
0 0
1 0

mothur > system(grep Id test_countendsT.dist)
Id_1_endgap Id_1 0.005435

mothur > system(grep Id test_countendsF.dist)
Id_1_endgap Id_1 0.005435

2

This is a bug that we recently discovered - sorry! However, if you replace the terminal -'s with .'s it should work. I think the default in mothur is to do this, but if you created your own alignment it may not insert the .'s at the beginning and end of sequences to indicate missing data. This should be incorporated in the next release of mothur, which will be released in the next week or so.