Interactive Phylogenetic Trees
About Interactive Phylogenetic Trees
Interactive Phylogenetic Trees enables authors to show phylogenetic trees below the article abstract on ScienceDirect.
Benefits for authors and readers:
- With Interactive Phylogenetic Trees, authors can enrich their articles with interactive data, expanding the possibilities of communicating the article’s content and improving its reading experience.
- It gives the reader quick and direct access to interactive phylogenetic data related to the article, helping them see the article in its broader context and improving their reading experience.
Molecular phylogenetics of Oestroidea (Diptera: Calyptratae) with emphasis on Calliphoridae: Insights into the inter-familial relationships and additional evidence for paraphyly among blowflies – Molecular Phylogenetics and Evolution
Structural and functional characterization of neuropeptide Y in a primitive teleost, the Japanese eel (Anguilla japonica) – General and Comparative Endocrinology
Interactive Phylogenetic Trees support Newick and NeXML data formats.
- A commonly used data format for representing phylogenetic trees
- It is used by many phylogenetics software packages, including PAUP*, GARLI, MrBayes, PHYLIP and TREE-PUZZLE
- You can use software packages like PAUP* and FigTree to convert other tree file formats to Newick
- Newick files must have the extension .new or .nwk (please note that a semicolon is needed to end the tree)
- Please do not enclose comments in Newick files and also delete any artificial line breaks within the tree data because these will stop the tree from showing
- A new exchange standard for representing phyloinformatic data
- NeXML read and write abilities are implemented in a number of software applications, including Mesquite, phylobase package for R and DAMBE
- You can also convert other tree file formats to NeXML using NeXML conversion utilities
- The file extension should be .xml (tree data submitted with other file extensions will not be processed)
- Please do not enclose comments in the file
Please note: tree data submitted in other formats will not be processed.
How to prepare taxon labels (as also recommended by TreeBase) :
- Make sure that taxon names in the tree file match the corresponding figure in the article
- Avoid using quotation marks, brackets, parentheses, commas, colons and semicolons
- Do not abbreviate taxon names (e.g. write "Homo sapiens" not "H. sapiens")
- Avoid using codes for non-redundant names (e.g. write "Drosophila melanogaster" not "DMelan45GRX”)
We strongly recommended you validate your Newick and NeXML files before submitting them, using our online validation tool.
- For optimal performance, please use Internet Explorer 9 or Mozilla Firefox 4 and higher
- Copy the entire content of your Newick/NeXML file and paste the data in the space provided
- Click on "Display tree" to see what the tree will look like
Please only upload your tree data to the online submission system if you are satisfied with the phylogenetic tree rendering provided by the validation tool.
You can upload your files separately via the online submission system, using the "phylogenetic tree data" submission category. Alternatively, you can submit as a supplementary file, depending on the journal (for details please refer to the journal’s Guide for Authors).
In your manuscript, you can indicate where you want the material to appear in the article, for example by writing ‘NeXML file 1 here’.
Interactive Phylogenetic Trees will feature in the online version of your article. Readers will be able to download the original tree files using the viewer. The PDF/print version of your article will feature static figures only (if the figures are included in your manuscript).
Reviewers will find NeXML files associated with Interactive Phylogenetic Trees in the supplementary material submitted with the manuscript.
- EES: the files can be downloaded via links on the final pages of the reviewer PDF
- EVISE: the files can be downloaded directly from the system [details TBC]
For more information, read the general reviewer instructions.