ReadSeq Limitations

Input format limitations/specifications

* GCG--only one sequence is allowed at a time.
* DNAStrider--the first sequence in a multiple sequence file is
   correctly converted, but the name of each of the remaining sequences is
   replaced with "### from DNA strider".
* Fitch--requires at least 20 bases in your sequence, otherwise ReadSeq
   cannot interpret the format.
* Phylip3.2--there can be no blank lines before the data, and for
   multiple sequence files with sequences longer than 20 bases, the sequence
   data gets jumbled together from the different sequences and the sequence
   names are not distinguished.
* Phylip--there can be no blank lines before the data.
* Paup/Nexus--when the sequences are converted, the title is truncated
   after any punctuation, and the truncated part is added onto the sequence,
   which leads to potential errors.

Output format limitations

* The following output formats truncate the sequence name (if performing a
  sixframe translation or a reverse complement, the reading frame and reverse
  complement information that have been added to the sequence name are
  truncated).  In addition, the first three formats also truncate the sequence
  data if there is more than one sequence and the sequences are not of equal
  lengths.
     *Phylip3.2
     *Phylip
     *Paup/Nexus
     *MSF