Currently, Bioinformatics recommends this new general template. Unfortunately it has very different styling from the final/classic layout below, but I had to switch out my original template to the general one on submission, so best to use that one by default now.

For convenience, a zip of the new template is here, so that cloning the Overleaf template isn’t needed.

For Bioinformatics, the sheet linked on this page indicates that the following documentclass invocation should be used:

\documentclass[numsec,webpdf,modern,large]

Also, add the following line:

\bibliographystyle{abbrvnat}

This repository contains a cleaned up latex template for Oxford Bioinformatics that can be used for preprints. It has not been used yet for an actual submission so use at your own risk.

The starting point (initial commit) is the version on Overleaf here. See the git history or remarks below for a list of changes.

It seems that the overleaf package I based this on has changed meanwhile. I copied things from there in September 2022 (see the initial commit here), but the ‘last modified date’ on Overleaf is listed as April 2022. Very confusing.

Either way, it does seem that newly published papers look more like the current version of the overleaf template rather than the one used here. But they are still not identical. It’s very confusing.

Clone this repository or download it as zip and run make from the repository root to start latexmk in preview-continuously mode.

Original	Revised

• Remove OUP from front page footer, and add copyright symbol for even first pages.
• Remove Bioinformatics and image from front page header, remove \access and \appnotes.
• Remove crop markers and change physical page size to 11truein by 8.5truein.
• Change abstract and top rule to be the full page width.

  NOTE: Published papers are inconsistent here. Compare the WFA paper with the Edlib paper.

• Empty \subsection{}, \history{}, and \access{}.
• Add T1 font encoding to fontenc package for smallcaps support. NOTE: This changes the size of em.
• Fix a typo in the sans-serif font used in captions. This changes captions from serif to sans-serif, and fixes italics and smallcaps inside captions. See tex.stackexchange.

  NOTE: Some published Bioinformatics papers seem to still have the wrong serif captions.

• Redefine \paragraph{title} to print the paragraph title in bold, followed by a period.

• Move text from main.tex into paper/*.tex.
• Add a bunch of default packages to paper/header.tex, including hyperref for clickable links.
• Rename document.bib to bibliography.bib, and remove unused plain.bst.
• Add appendix.