what is the maid_dir?
The $ prefix to maid_dir indicates that it is a Perl scalar variable. See Variable names. The name of the variable would lead me to suspect that it contains a directory name or path.
If that does not adequately answer your question, you should provide more context: show a small, self-contained code example with expected vs. actual output.
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From this tiny little glimpse, $maid_dir."\\".$maid."aln_hu.aln", note the concatenation "." operator, so there is a path to a file in the directory $maid_dir, this file is $maid appended to it is the postfix aln_hu.aln - .aln is the Clustal reports files format in Bioinformatics sequence alignment-
$maid_dir = 'C:\Documents and Settings\Blast_Clustal';
$maid = "report";
print $maid_dir."\\".$maid."aln_hu.aln";
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-file => $maid_dir."\\".$maid."aln_hu.aln",
It's also, IMHO, a more roundabout way of saying
-file => "$maid_dir\\${maid}aln_hu.aln",
These old eyes get watery having to parse all those dots and quotes.
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