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I want to convert an existing website for mobile version, what will be the best choice for me.
You would need to provide a lot more information about your goals and your background to answer the best solution for you.
However, I can clarify your title: PhoneGap is a complementary solution to jQuery Mobile. They provide different capabilities and work together. You can use one or both of them. Here’s a picture.
PhoneGap does two major functions:
Converts JavaScript/HTML/CSS assets to a native app
Provides a set of JavaScript APIs that map to device capabilities, not otherwise accessible to a web app, like Contacts, Accelerometer, Telephony, GPS, etc
jQuery Mobile is a cross-platform user interface system. It is an extension to jQuery that provides a set of UI libraries specialized for mobile device programming including small screens and touch and swipe events.