yeap the file is clastalw2.exe and NOT clustalw.exe as written on perl error.I was cleary searching for wrong file.

If I C:\> where clustalw2.exe I get eventually: C:\Program Files (x86)\ClustalW2\clustalw2.exeSo I can find the executable by command line. But

 'C:\Program Files (x86)\ClustalW2' is the same i use from the beggining, and even though I ve put ENV{CLUSTALDIR} on the script and add it to Windows Path variable i have this error..

Try creating a shortcut clustalw.exe to C:\Program Files (x86)\ClustalW2\clustalw2.exe


or add this line to your code

$Bio::Tools::Run::Alignment::Clustalw::PROGRAM_NAME = 'clustalw2';
poj

by adding this line:

'C:\Program' is not recognized as an internal or external command, operable program or batch file. ------------- EXCEPTION ------------- MSG: ClustalW call (C:\Program Files (x86)\ClustalW2\clustalw2.exe align -infile="C:mplamplamplamAppData\Local\Temp\mmbu9X1Xk7\_L046A68Sd" -output=gcg -matrix=BLOSUM -ktuple=3 -outfile="C:mplamplampla\AppData\Local\Temp\mmbu9X1Xk7\QsDsDa0tAB" 2>&1) crashed: 256 STACK Bio::Tools::Run::Alignment::Clustalw::_run C:/Strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Clustalw.pm:768 STACK Bio::Tools::Run::Alignment::Clustalw::align C:/Strawberry/perl/site/lib/Bio/Tools/Run/Alignment/Clustalw.pm:515 STACK toplevel C:mplamplampla\c3.pl:28

You mean creating a shortcut of clustalw2.exe and rename it to clustalw.exe? By the way Windows doen't let me create shrotcut in this folder. Suggested me putting the shortcut to Descktop.