Choosing bioinformatics methods

I read a paper that uses different software. What should I choose? Can I use a different version of software than described here?

Making decisions about analyses:

• what algorithms
• parameters
• compute methods (see choosing_compute.md)

Why use a particular method?

• Other people in the lab use it (consistency with previous analysis, for comparison purposes)
• Other published literature uses it
• Published literature comparing methods says it’s appropriate
• software manual says it’s the best way