Is there a way to use phpmyadmin if my Magento installation is on vagrant box? Or any recommendations for other tools?
Using command line is horrible if you are working with large tables.
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Yes of course, just download and chuck in phpmyadmin in your work directory or use adminer https://www.adminer.org/ which is a single file that will enable you graphical interface to your database. Now access it through url e.g. example.com/adminer.php and use your database credentials to log in