The Square card reader allows anyone with an iPad or smartphone to accept credit card payments with a single swipe. Photo: Lisa Wiseman

SAN FRANCISCO — What’s better: A piece of software designed specifically to run on one device, or a web-coded experience that can be accessed on any gadget equipped with a browser?

Keith Rabois, chief operating officer of mobile-payments startup Square, says going ‘native’ — or using devices with apps made specifically for one platform — is crucial when launching an application on a mobile device.

“If you care about the user experience…it’s almost impossible to deliver that with a non-native application,” said Rabois at the MobileBeat technology conference on Tuesday.

The debate between web-based apps versus those made for specific platforms has been long and heated. Companies like Apple have proprietary coding languages (Cocoa and CocoaTouch) tailored to its iOS mobile platform. So for example, if a developer decides to create an app only using Apple’s code, you’re not going to see those apps on any devices besides Apple’s; if you’ve got an Android phone, you’re out of luck until the developer studio ports it over to Google’s platform.

HTML5, however, offers an alternative to programming in a native, platform-specific language. Using open, freely accessible web development protocols, programmers can write in HTML5. That means any device you own that runs with a browser — be it desktop or mobile — can access the content.

Google is especially pushing the web-based tools, as HTML5 content is searchable by Google’s crawling indexing systems — that means you’ll be able to look for what you want in a Google query. And the very popular internet radio service Pandora launched its HTML5-powered version of its site on Tuesday as well.

But there are disadvantages in going with HTML5. There’s often noticeable speed decreases in accessing browser-based content, as well as problems with utilizing other parts of a phone or tablet’s hardware (like Bluetooth, for example). Essentially, you’ll be missing out on some of the cooler features specific to, say, an Android or iOS device.

And of course, there’s the curated, centrally located application markets like Android’s Market and Apple’s App Store. One quick stop at either offers you a buffet of application choices. Payments are also streamlined, as Apple has your credit card info and Google offers direct-carrier billing options. With HTML5 browser-based content, you may have to enter all of your payment info over and over again each time.

“Being installed with an icon on an iPad is pretty damn important. People see my iPad all day long,” said Rabois. “They don’t necessarily see a computer screen all day long.”

Rabois echoes the philosophy Square has taken in its approach. The app is available in both the Android Market and Apple’s App Store, and is focused on smaller merchants who opt for mobile-based points of sale rather than a traditional cash register.

Created by Twitter co-founder Jack Dorsey, in May of 2010 Square debuted its card reader, literally a square-shaped plastic dongle, which attaches to both Android and Apple smartphones, as well as the iPad and iPod Touch devices. After installing the Square app software on your device and going through a brief identity check, you’re up and running, ready to accept credit card payments from customers.

Square has been active in the mobile payments space. In May, the company launched Square Register, a software interface built specifically for merchants to track their inventory and sales from their smartphone or tablet. On the customer side, Square also launched its ‘card case’ software, which literally lets you pay for items with your smartphone at retailers using Square’s Register software. The company has registered “hundreds of thousands” of merchants, and has processed over $66 million in transactions in the first quarter of 2011.

Google also launched a mobile payments initiative recently with Google Wallet — a virtual wallet which stores your credit card information on your phone, and uses Near Field Communication technology to interact with point-of-sale terminals through a simple wave of the smartphone.

Companies like Square and Intuit, however, have an advantage over Google, as NFC technology isn’t quite mature yet. “Near Field Communications might take a couple of years to roll out fully,” said Matt Marshall, founder of the technology blog VentureBeat, at the MobileBeat tech conference on Tuesday.

And unlike the infant NFC technology, Rabois says native apps are growing more and more responsible for providing content to users, catching up to the Web at a faster pace. Rabois claimed 33 percent of searches on Yelp — a local merchant and retail recommendations service — came from the ten percent of iOS app users with the Yelp app installed.

Ultimately, installing apps on our mobile devices is becoming more of a personalized experience, according to Rabois — moreso than the web.

“The decision to install an app is partially utilitarian, and partially self-expressive,” Rabois said. “It says something about myself.”