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You can remove index.php from url in magento by following ways.
Then use the following steps
1) Login to admin section by using the URL
http://domain.com/index.php/admin
2) Then go to “System >> Configuration >>Web >> Search Engines Optimization”
Use Web Server Rewrites : YES
3) Go to “System >> Configuration >>Web >>Secure”
Use secure URL Frontend: YES
4)Then create the .htaccess file under your the magento installed folder.
If the magento installed under document root ( /home/username/public_html) then add follogig rules into .htaccess file
RewriteEngine On
RewriteBase /
RewriteRule ^index.php$ – [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
and If the magento installed under /shop or directory then add the following rules into ” /home/username/public_html/shop/.htaccess ” file.
RewriteEngine On
RewriteBase /shop/
RewriteRule ^index.php$ – [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /shop/index.php [L]