Links to broken features reside in the inc/menuprocessing.php, selectFeatureAnalysis.php, and selectParticleAlignment.php
selectParticleAlignment.php:
IMAGIC Multi Reference Alignment (requires IMAGIC and the template stack thing, below)
CAN Reference-free alignment (runs but does not upload results)
selectFeatureAnalysis.php:
Cluster by Affinity Propagation (works but broken on large stacks)
IMAGIC Multivariate Statistical Analysis (dependent on IMAGIC version)
inc/menuprocessing.php: CTF Estimation
CtfTilt Estimation (works and uploads, but fails alot; there is a warning)
inc/menuprocessing.php: Particle Alignment
Template Stacks (this is Dmitry's thing)
inc/menuprocessing.php: Refine Reconstruction
See Refinement_Package_Status
Frealign Refinement (almost)
SPIDER Refinement (broken)
Xmipp Refinement (broken)
IMAGIC Refinement (broken)
inc/menuprocessing.php: Tomography
inc/menuprocessing.php: Region Mask Creation
Does any of this work? Anchi may know.
Crud Finding
Manual Masking