Tree Builder FAQ

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Is there a tutorial on how to use Tree Builder?
The Tree Builder tutorial is here.

Is it possible to upload sequences that are not in FASTA format to be used in the Tree Builder tool?
Our tool currently only take the sequences in FASTA format, which is the most common and simple format for sequence data.

How long should my sequences be?
It is best to select full-length or near full length sequences (> 1200 bp) as the reference sequences to build the tree with.

I cannot generate a tree using this program. What is wrong?
The tree builder is a Java applet. Make sure that your browser is java-enabled before contacting us.

How do I construct phylogenetic tree using sequences from my BLAST searches?
You can import these sequence into your myRDP account to build your trees.

Can I save a tree in myRDP that I can edit later?
RDP does not currently have the online function to save the tree in the myRDP nor a sophisticated tool to edit the tree.

Is there a downloadable version of Tree Builder?
We do not have standalone distribution package of treebuilder in RDP. Neverthelss, you can download the parts to run. The treeing program is Weighbor. The distance matrix can be calculated by dnadist (PHYLIP) or the tool in the pyro pipeline (Mothur: Phylip Distance Matrix for <50000 sequences). If there are too many sequences, you can select representatives using the pyro tool, Dereplicate.

The outgroup pull down remains blank when I have them selected. What should I do?
This problem is most likely caused by the presence of some illegal characters such as & or " in the header line of the sequence records in the uploaded fasta file. These characters tend to mess up with the functional characters in a HTML file. Files should contain only letters, numbers, underscores, and dashes before uploading.

What does the scale bar mean?
The scale bar on the tree represents the measure of phylogenetic distance. It is calculated as the ratio of nonidentical base positions to all base positions disregard of positions in which gaps are present in the pairwise alignment. It is also can be defined as the percentage sequence dissimilarity between two sequences. The given bootstrap value is times out of 100 tests. The unit of distance is times of base substitutions per 100 hundred positions. So, '0.1' means 10 base substitutions per 100 positions

I'm building a tree using the NCBI taxonomy ids to identify organisms. How do I convert the sequence identifiers to the NCBI taxa id of their organisms?
The names/ID/definition can be switched back and forth using the keystrokes CONTROL-N(for NCBI accession), CONTROL-D(NCBI definition), and CONTROL-I (RDP ID).

After uploading my sequences and utilizing the SEQMATCH function my sequences produce a S_ab score but the similarity score says "not calculated". How can I get a similarity score for these DNA sequences?
Pairwise similarity values are only calculated by SeqMatch IF the sequences have been aligned by RDP. Any sequences DIRECTLY selected from RDP through Hierarchy Browser or from myRDP aligned sequences will have pairwise similarity values calculated and displayed by Sequence Match. The query sequences through copy&paste or file uploading to Sequence Match will not display the similarity values.

I keep getting an error that says "Sequences in the 1st column share less than 200 comparable positions with sequences in the 2nd column".
The tree can't be calculated because there are sequences that do not share enough comparable positions. The tree is calculated based on a distance matrix that contains distance values from all pairs of sequences. If there is even a single pair of sequences that do not overlap over 200 bp positions, there is no distance value for this pair and the tree can't be calculated.

Do you offer pre-built reference phylogenetic trees?
RDP does not currently offer a pre-built phylogenetic tree. For a list of sequences you already have the sequence identifiers (either NCBI or RDP), you can select them on RDP's Hierarchy Browser via uploading them through seqcart. After this, you can build the phylogenetic tree using Tree Builder. For sequences not yet in RDP, such as your own sequences, you can upload to your myRDP. account, which automatically aligns them. Then you can select them from inside of your myRDP and build a tree.

I have more than 200 sequences and used the pyrosequencing pipeline. How do I create a tree from this output?
You need to calculate distance matrix with the tool and run Weighhor from your computer if you want the same type of tree as RDP's.

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