This interface was developed to visualize data pertaining to positive selection in genes. However, it can be used for a broader range of purposes. As long as the data contains a Newick-formatted tree file, a FASTA alignment file and a results file organised in columns (with site numbers as the first one), the Python script used to generate the XML file used by the interface will work.
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Python
- biopython
- lxml
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Node.js
- npm
On the homepage, upload your three files on the required fields:
- Newick-formatted tree
- FASTA alignment
- Statistical results
If your data requires specific parameters, you are free to change several options:
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A toggle to choose whether your sequences should be treated as nucleotidic (and translated into proteins) or not
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A toggle for the logarithmic transformation of branch lengths (can be useful to create space in the tree if some branches are really short)
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Which column to use for the results (site mode)
Once you are done, just click the Display button and the visualization will be available.
The layout is as follows:
- Tree on the left
- Results histogram and alignment on the right
Parameters include:
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Which sequence type to display (amino acids / nucleotides)
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Choosing between thresholds for computations
- "<" will look at values below the lower threshold
- ">" will consider values above the upper threshold
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In branch-site mode, boundaries that are used to compute branch colors
- If you want colors to reflect the local aspect of branches, you may enable the "Update on scroll" option
- "Reset" replaces the current values to account for the whole sequence