There are a number of data analysis software packages available for free. These are listed below, with links.
For novice users, we recommend working through the tutorial provided by Relion. This tutorial is very comprehensive and will give you a good feel for the overall data analysis workflow and allow you to practice on an “easy” data set before you get started! Note that other programs also provide tutorials which are helpful in learning their individual interfaces.
For the more experienced user, we find that each software has its own quirks and some work better on particular types of data than others. Depending on your project, you may want to use one or more of the available packages out there. Most packages can be used in combination with one another, but be aware of issues that can arise from switching between different data formats!
In general, we have found that Cryosparc is good for fast data analyses, and Relion provides the most comprehensive analysis toolkit. CisTEM is optimized to run on CPU only, so this is a good choice if you do not have a GPU machine. Users with hard to pick particles may find the crYOLO picker (part of SPHIRE) particularly useful. Ultimately, the choice of software is up to you!
EMAN2 (recommended for analysis of negative stain data)