Thanks to Torsten Seemann for bringing this to my attention…

In 2003 a bioinformatics tool was published. A tool with a thoroughly sensible name and acronym:

BIBI: a Bioinformatics Bacterial Identification Tool

A simple name with a simple, and not-too-bogus. initialism. Bravo. However, a subsequent update to BIBI brought about a change to the name:

^le BIBI:

Where the 'le' refers to 'light edition'. It should be said that most references to this tool drop the superscript notation for 'le'. Let's move forward to the present day and the publication of another version of this tool:

leBIBI ^QBPP : a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences

The full expansion of this new name is as follows:

Light Edition Bioinformatics Bacterial Identification Tool Quick Bioinformatic Phylogeny of Prokaryotes

Quite a mouthful! Bonus points for including 'Bioinformatics' and 'Bioinformatic' as part of the same name, as well as the largely redundant inclusion of 'Bacterial' as well as 'Prokaryotes'.

Generally I find use of superscript in software names to be largely unnecessary. It can make the tool name harder to read and it is unlikely to reproduced verbatim by others who mention your software. Starting your software with a lowercase letter also means that this might appear in uppercase if used to start a sentence (as happens several times in the above paper). Not a terrible problem but it reduces the strength and consistency of your 'bioinformatics brand'.