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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