Increase this and gaps will get shorter. If transitions are unweighted, then all nucleic acid mismatches have the same weight. Don't forget the title in line 1 of each seq- uence file. Upper or lower case may be used. No ambiguity codes are used.
Residues are either a valid amino acid or nucleotide or unknown.
The default file name is derived from the sequence input file, with the extension .DND added on. The dendrogram is a description of the relatedness of the sequences in the data set. You can use a dendrogram file immediately for a multiple alignment or use it again at a later date, to save having to generate it again. Also, you can edit the file to change the branching order of the sequences. There are 5 columns of numbers.