Image via [Wikipedia](http://commons.wikipedia.org/wiki/Image:Victorinox_SwissChamp.jpg)
Yes, DIALIGN-TX has all the problems with scientific software. All of them in 1.8 Mb of data, and I’m being kind. Let me explain that. I have this small project, and DIALIGN-TX is one of the programs I want to check. I compiled fine, or so I think: it runs ok on the Mac, shows me the parameters to run it, in a large list of options. Most of these options have a “DEFAULT” value, which means they are not needed to run the program. And there’s an usage example
Usage: dialign-t [OPTIONS] 
(notice the error on the usage, I just copied and pasted)
I tried every possible combination, with and without options, setting and not setting them, with different input files, no one worked. Then I decided to read the documentation. No true. First I decided to get the documentation, nowhere to be found. The I rechecked the website. Nada. Then I googled it. Nada to the power of 2. Then I tried the command line options list again. Nothing worked. Now, the next step is to try on a different operating system (I will update here).
But why did I state that it has all the problems of scientific software in one tarball? Well, it has the main problem of scientific software: it’s used as a mean to achieve the largest number of publications possible, and that’s it. There’s no documentation, no support on its website whatsoever. If you want to run it, you’re out there in wood by yourself with your little pocket-knife and a compass. It’s a miracle that I was able to compile it.
If I weren’t interested in running this software (for scientific reasons) and were a little bit less computer savvy, would I elect to use DIALIGN-TX in my research? Not in 1 billion years. No wonder why people stick to ClustalW and ClustalX. They are well documented, everyone knows it, and you can run in any system as it is pre-compiled for them. In the meantime DIALIGN-TX is still a niche alignment software, that maybe (I don’t know) no one uses it.