Dalzeil (Dark/Light): Single function to toggle between the light and dark modes of the user interface. It can live in your dock and provide instant access to an interface switch. There are more sophisticated solutions available, but Dalziel is simple and free. Download.

Coulson plot generator: An open source Java application for creating a multiple pie chart diagram and comparing subunit occupancy across a range of entities. The number of pies, segments, labels, and colours are customisable. The CPG creates an editable PDF from a separate text file (.csv) and has zoom capability for larger datasets. This format is particularly useful for visualising patterns in big data. Originally developed for comparative genomics, the Coulson plot is appropriate for displaying other hierarchical data. The format was conceived by Richard M. Coulson and coded as an application by Helen I. Field. Icon design by MCF. Note that Apple broke this some time ago so the Mac version runs on Mavericks as the latest OS. Available as binary or source code at GitHub. Probably superseded by R.

RNAit2: Web-based tool for the identification of primers for RNAi in kinetoplastids. The software uses Primer3 to predict suitable primers for PCR and then checks whether the predicted product has off-target potential. The data are returned for the user to assess, and the settings are customisable. RNAit was originally developed by Seth Redmond, and the present iteration was recoded by James Abbott at the University of Dundee and runs with a Python backend within a virtual machine; the data are therefore completely private; we collect no logs. The RNAit2 source code is available on GitHub. The link to the software is here.

WCAIR omics hub: Identifying orthologs - genes sharing an ancestor in different organisms - is vital to assigning functions to unknown proteins, and identifying best candidates for crystallisation, to finding opportunities for pathogen hopping and identifying potential compound off-target effects. Currently there are many tools available for ortholog identification but all have various limitations including organism availability, scalability, command-line knowledge and issues with divergence leading researchers to use manual best-reciprocal BLAST, a highly time consuming and unscalable method.To combat this, we have created the WOH, a website which automates manual best reciprocal BLAST drastically reducing user time from months to minutes. Developed by Erin Butterfield. Details here.

LECAprot: An ancestral reconstrution of the Last Common Eukaryotic Ancestor proteome, and a searchable resource. All coding and strategy by Lael Barlow.

If you use CPG or RNAit in a publication, please cite as follows:

Field, H.I., Coulson, R.M.R., and Field, M.C., (2013) ‘An automated graphics tool for comparative genomics: The Coulson plot generator.’ BMC Bioinformatics 14 141

Redmond, S., Vadivelu, J., and Field, M.C., (2003) ‘RNAit: An automated web-based tool for the selection of RNAi targets in Trypanosoma brucei.’ Molecular and Biochemical Parasitology 128 115-11

Details for WCAIR omics hub, and where to obtain source code and setup were published here:

Butterfield, E.R., Abbott, J.C., and Field, M.C., (2021) 'Automated phylogenetic analysis using best reciprocal BLAST.' Methods in Molecular Biology 2369 41-63