Phylogenetic Trees

About Phylogenetic Trees

You can display interactive phylogenetic trees in Newick and NeXML format in your online article on ScienceDirect. They will be visualized below the abstract. Readers will be able to download the original tree file.

The PDF or print version of your article will not automatically include an image of the interactive phylogenetic tree. If you'd like these versions of your article to include a figure of your phylogenetic tree, please include an image version as a figure in your article.

Example Articles

Author Instructions

Preparing

We support Newick and NeXML data formats. Tree data in other formats can also be submitted, but will not be visualized, just made available for download.

Newick is 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.

To ensure optimal rendering of Newick files:

  • they must have the extension .new or .nwk
  • note a semicolon is needed to end the tree
  • please do not enclose comments
  • please delete any artificial line breaks within the tree data

NeXML is an 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.

To ensure optimal rendering of NeXML files:

  • the file extension should be .xml
  • please do not enclose comments

For preparing your taxon labels, please:

  • 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 encourage you to also upload your tree data to relevant data repositories, such as TreeBase and Dryad.

Previewing

We strongly recommend you validate your Newick and NeXML files before submitting them, using our online preview 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

Submitting

Please only upload your tree data to the online submission system if you are satisfied with the phylogenetic tree rendering provided by the preview 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’.


Reviewer Instructions

Reviewers will find Newick and 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.

For more information, read the general reviewer instructions.