When you export your InDesign layout with in5, the output is full HTML5 as opposed to an animated GIF. An Animated GIF is a single image file, made of limited colors...that's why the in5-exported HTML5 content is clearer than the GIF. 

When you use the in5 Animated GIF Maker, the animation created in InDesign and exported as HTML5 is recorded and saved as an animated GIF, a lossy format (meaning some information is dropped to reduce file size) with an extremely limited color palette (256 colors versus other images which may have millions of colors).

You can improve the quality of your animated GIF by keeping that limited color palette in mind when you create your animation. For example, some InDesign animation presets such as Fade in cause pixelation because each frame that includes the fade transition may be creating additional colors which takes up spaces in the limited color palette just for the transition between opaque and transparent. The limited palette is used across all frames in the animation so having a custom color just for a transition that is barely onscreen takes away from the color quality of the frames that have more impact on the over feeling of image quality.

Try the following steps to see how they affect the quality of your GIF:

  1. Reduce the duration of animations that change opacity settings
  2. Replace animations that change opacity settings to a different animation preset
  3. Test various Dithering settings in the in5 Animated GIF Maker
  4. Test various levels of compression in the in5 Animated GIF Maker following the recording (try setting it to None or to one of the lossless compression settings)

Also, as a general rule of thumb, don't expect photographic images to work well in animated GIFs. By their nature, photographic images include millions of colors and don't translate particularly well to a format limited to 256 colors. Illustrated images will a fixed number of colors tend to work much better in GIFs.

If you're making an ad, check if it can be HTML5. If so, you might consider keeping the content as HTML5 and exporting as a Google Ad:

If the content is HTML5, then you won't need to convert it to an animated GIF.

Getting a deeper level of color control

To get the most level of quality control in your GIF, you can also use the in5 Animated GIF Maker to convert your HTML5 content to an MP4 video, which you can then open in Photoshop, optimize for color, and save as an animated GIF. Here's a video where Justin shows the process: