Known Issues ============ We are working on addressing the following issues in a future release: * MACSE marks the presence of stop codons in the AA sequence with a '*' but does not mark stop codons in DNA sequences. From the MACSE paper: "... at the nucleotide level, MACSE uses the symbol ‘‘!’’ to represent deletions of one or two nucleotides that induce frameshifts and it uses no special representation for the stop codon." In multalign.remove_frameshifts, we can truncate sequences at the first stop codon found in the AA sequence, but doing so for DNA sequences is harder (it requires considering all of the possible frames). Currently, we do not truncate the DNA sequences at stop codons. * Annotated contigs from the transcriptome pipeline are sometimes misformatted and missing the sequence. * Some SwissProt descriptions are messy, and contain multiple '>' characters, which can confuse programs that look for '>' as the ID line delimiter for FASTA format. We plan to replace the '>' with another character in the Agalma-optimized SwissProt database.