I am looking for an open source software that has been widely used in the past and current with biologist, I am a software graduate student and my main focus is on scientific software testing. Greatly appreciate if you can name some of the open source commonly used software in your community ?
Edit: So the main purpose of this query "Finding the most commonly used software" is to run some software tests on source code and see if we can help and improve open source software.
Have a look at the Biostars tags: https://www.biostars.org/t/ and try to extract only those tags which are software:
Then you get
- R ahead of
But R and Python are also programming languages (and have an 'unfair advantage') which you can do a lot of different things with, therefore blast is -not surprisingly- the tool Biostars' users have most questions about.
To add one more data point to your survey, here's my selection from top of my head
macs (peak caller)
I deliberately left out general purpose tools like R, python, unix command line tools etc.
Take a look a the Nature's top 100 for a historical view: http://www.nature.com/news/the-top-100-papers-1.16224
Interestingly, the Clustal W paper is ranked above BLAST, though there are several BLAST and Clustal papers so I think BLAST is collectively higher. Either way, both have had a large impact on the field but timing is a major factor in popularity, especially in the citation statistic.