Yellow Fever Virus Phylogenetic Typing Tutorial
One or more (up to 20000 per run) Yellow Fever sequences can be pasted (A) or uploaded (B) in Fasta format (see Fig. 1). Sequences of all regions of the Yellow Fever genome can be used.
When pasting a single sequence the Identifier of the sequence (>Sequencename) should be included (Fasta format). One example sequence is present as a default. A set of three example sequences is also available.
Fig. 1. The startingpage of the Dengue typingtool
The analysis takes up to a few seconds per sequence. Thus, for large batches the run can be viewed later, by typing the Job-Id at C. Here also runs by others can be viewed, if the Job-Id has been communicated. Runs are kept on the server for 1 week.
Fig. 2. Overview of the results
After the 'Start' button is pushed the analysis is started and after a few seconds the results overview is shown (Fig. 2). While the analysis is still in progress the following message is displayed: 'Analysis in progress... (Showing partial results). This page will be automatically updated every 5 seconds...'.
The Job Id number, which can be used to retrieve the results later is displayed at the top of the page as soon as the job is started.
For each sequence the length, positioning on the Yellow Fever genome and assigned genotype are determined.
After the complete analysis is finished the analysis results can be downloaded as XML, CSV or Excel file.
For each sequence more details can be viewed in the individual reports by clicking on 'report' in the results table.
The report of the genotyping details per sequence contains a brief overview of the assignment, followed by details of the phylogenetic
analysis including a phylogenetic tree.
The report contains information on:
- The sequence submitted (name and length)
- Blast result: The genus/species (Yellow Fever species) of the submitted sequence
- Phylo result: For Yellow Fever sequences, the genotype assignment
- The robustness of the phylogenetic assignment using bootstrap values. Only with bootstrap > 70 a genotype or variant is assigned.
- A graphical representation of the Yellow Fever genome showing the genomic region of the query sequence with the start and end positions related to the Yellow Fever reference sequence.
- A NJ tree is computed with the submitted sequence at the top.
- The bootstrap tree can be viewed and downloaded in the PAUP* log file
- The alignment can be downloaded in NEXUS or FASTA format
No genotype is assigned if:
- The submitted sequence belongs to another Flavivirus genus. In this case the genus is indicated and the analysis stops.
- The submitted sequence is shorter than 150 bp. In this case only assignment of the species (Yellow Fever) is possible.
- The bootstrap value < 70. In this case an alignment and a NJ tree are produced which can be used to get an indication of the phylogeny.
At the end of the analysis, it creates a phylogenetic tree with all of the query sequences and the reference dataset.
Fig. 3. phylogeny of 6 novel sequences analyzed with the reference dataset in the YFV typing tool. Blue cluster - South American Genotype I; Red - South American Genotype II; Green - East African Genotype; Orange - West African Genotype.