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Flot is a pure JavaScript plotting library for jQuery with a focus on simple usage, attractive looks and interactive features


Highcharts is a Javascript charting library that uses HTML, SVG, and VML



Highcharts is svg and as such it is much more dynamic than flot you can restyle graphs with css attach events perform animations etc..

from question  

JavaScript Charts API: Flot jQuery Plugin OR Google Visualization?

Also flot does a better job to synchronise common axis scale with many series;highcharts does a really good job here mixing bubble chart with other kind of series but isn t free for us government context

from question  

Embed bubble charts on a web site

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