Image via [Wikipedia](http://commons.wikipedia.org/wiki/Image:Hemagglutinin-alignments.png)
There’s always the right time for everything. And for some scientific software it’s time for retirement. I will give here a one examples, but I bet if you’re a bioinformatician you will have others, and if you’re something else you will scratch your head and think “This guy is right!”. So let’s see the case of ClustalW.
ClustalW was the first massively used alignment program and it’s a great program. But in my opinion it was a great program and has to be remembered as such, a great tool that introduced the mysteries of sequence alignment to so many people. It had everything, an UI, a command line, and more important it converted and many file formats.
A quick search on Google Scholar shows about 45000 results for ClustalW, but I’m sorry, it has to go. You have to stop using it, please. If you’re a bioinformatician, stop supporting it, don’t create a ClustalW(X) wrapper on any tool, forget about it. Every time someone mentions the word Clustal in front of you, pretend that he/she is a creationist. If you are not a bioinformatician, ask your local bioinformatician what is the best tool to use (Muscle, MAFFT and ProbCons are my favourite), delete the ClustalW on your HD (save one for posterity) and start living the high-alignment-life.