Just wanted to note some ambiguous messages from the aligner when using “flip=t”.
Some of you sequences generated alignments that eliminated too many bases, a list is provided in sequences.flip.accnos. If the reverse compliment proved to be better it was reported. # cat sequences.flip.accnos CP002042 AJ867032 AJ867034 reverse complement did NOT produce a better alignment, please check sequence. AM261868
The above implies that the reverse-complemented sequences for CP002042, AJ867032, and AM261868 produced a better alignment than their original sequences, and were included that way in the resulting alignment. If this is correct, could you state that explicitly in these messages? From an end user perspective, it is not clear how these were ultimately treated (except for AJ867034, which is explicitly stated).