Use this tool for calculating a distance matrix from your alignment file. If your sequences are not yet aligned in the greengenes 7,682-character format, then first align them. Each correctly aligned sequence in your uploaded file will be pairwise compared using the DNAML option of DNADIST (PHYLIP package). The Lane mask (Lane, 1991) will be used to restrict calculations to 1,287 conserved columns (lanes) of aligned characters. The resulting distance matrix will be emailed to you. Please contact tdesantis@lbl.gov before uploading files containing more than 800 sequences.

Other notes:

• A, C, G, T 16S rRNA gene base frequency used by DNADIST (F84 distance) will be 0.2537, 0.2317, 0.3167, 0.1979, respectively.
• Transition:Transversion Ratio is assumed to be 2.0.
• Make sure the sequence identifiers in your file are 10 charaters or less.
• Sequence names may not contain the following characters ( ) : ; , [ ]

When finished, consider using DOTUR to examine your distance matrix, construct collector's and rarefaction curves and to cluster your sequences at various similarity levels.