Taxomatic FAQ

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What data sources can I use in the Taxomatic?
There are three choices for supplying source data; sequences selected from RDP, an aligned fasta file, or a DNADist file. When sequences you select from RDP are are used, only model positions are taken into account when calculating the distance matrix. When either RDP sequences are used or a fasta file is uploaded as the source data, a similarity matrix is computed for the selection using uncorrected pairwise gene frequencies. Uploaded fasta files should contain only comparable positions.

What can I use to display a distance matrix?
When displaying the distance matrix on taxomatic you may either use the RDP taxonomy or supply your own.

How do I use the RDP Taxonomy?
To use the RDP Taxonomy use sequences from your Sequence Cart or upload a fasta/dnadist file with RDP Sequence IDs. If you are using sequences from your myRDP account, you do NOT have to supply your own taxonomy; when your sequences are uploaded, they are classified for you. If you choose to upload your own taxonomy, it must be in the specified xml format (see below for an example).

How do I use my own taxonomy?
When you upload your own taxonomy, it will override any taxonomy information from the RDP (and as such, there must be a <Sequence> tag for every sequence that you want to use from the data source; sequences without taxonomy information will be ignored).
Here is a sample:

<taxonomy xmlns="http://rdp.cme.msu.edu/taxomatic" name="RDP User download">
    <Taxon id="780" rank="family" name="Chlorobiaceae">
        <Taxon id="792" rank="genus" name="Chlorobaculum">
            <Sequence seqid="S000779102" name="uncultured Chlorobaculum sp.; 16/3-110"/>
            <Sequence seqid="S000779116" name="uncultured Chlorobaculum sp.; i9-114"/>
            <Sequence seqid="S000779113" name="uncultured Chlorobaculum sp.; i9-9"/>
            <Sequence seqid="S000779099" name="uncultured Chlorobaculum sp.; 16/3-102"/>
            <Sequence seqid="S000779110" name="uncultured Chlorobaculum sp.; 16/3-167"/>
            <Sequence seqid="S000779120" name="uncultured Chlorobaculum sp.; i9-111"/>
            <Sequence seqid="S000779109" name="uncultured Chlorobaculum sp.; 16/3-165"/>
            <Sequence seqid="S000779101" name="uncultured Chlorobaculum sp.; 16/3-108"/>
            <Sequence seqid="S000779104" name="uncultured Chlorobaculum sp.; 16/3-119"/>
        </Taxon>
    </Taxon>
</taxonomy>
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