Does Anyone Know Of A Comprehensive List Of Bioinformatics Tools That Is Kept Very Up To Date?

Question

[seraphya]

Anyone know of a comprehensive list of bioinformatics tools that is kept very up to date?

The best I can find are:

• SEQwiki list,
• Wikipedia: alignment software,
• Wikipedia: Open source bioinformatics software.

Does anyone have any other lists worth checking?

The SEQwiki doesn't have information about when the software was released. The wikipedia alignment list has that information, but it only about a subset of tools. The Open source wikipedia list is very under-populated.

Answer 1

[Neilfws]

Lists of tools were popular in the 1990s. These days:

1. There are so many that maintainers cannot possibly curate a list (keep it updated)
2. There are so many that users cannot possibly browse a list
3. The pace of development means that new tools for your purpose are appearing (and disappearing) all the time

Rather than look for lists you should:

1. Look for the tools required to perform your current task
2. Develop your web searching skills; with the right query, the top hits will be the tools that you want
3. Follow the development of a few projects key to your field (e.g. R/Bioconductor)

[seraphya]

That is what I thought. If bioinformaticians are trying to curate lists of genes, proteins and ontologies can we really not curate a list of the tools we use?

There is already an ontology of the operations tools prefeform: http://bioportal.bioontology.org/ontologies/EDAM?p=summary

[Neilfws]

My point is that lists of software are neither useful nor desirable. And who wants to curate them? There is little if any reward.

Don't get me started on the worth of ontologies ;)

Answer 2

[Prakki Rama]

@seraphya You can get quite a few Arraydirectory

Answer 3

[Ian]

Not quite a database of tools, but the journal Bioinformatics has an annual publication of new and updated Webtools and Databases. There is an associated database of databases that is discussed at the start of the database issue.