Please take some time to read the documents before you run a program the first time. And please revisit the document pages once in a while because the documents as well as programs are being updated constantly. Even if you just suspect some problems in our programs, please don't wait till you are sure. We will be glad to hear from you under any circumstances. Many problems are due to misunderstanding or overlooking some rules.
Some rules are very simple but easy to overlook or forget.
For example, sequences in input to the mulple sequence alignment programs must be separated by header lines. Many people often forget the header lines. Some problems may come from your browser. Though, fortunately, most browsers can handle HTML FORM properly or in expected ways, you may use a browser that behaves differently. Unless we know about the problem, we simply can not do anything about it.