Protein
IQ
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Project
Inputs
Protein
IQ
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New batch
Batch setup
Tool
pySCA
Name
Project
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Inputs
Template
CSV / Excel
Paste CSV
Operation
Full SCA and sectors
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MSA
Files
FASTA
Add optional input
Max position gap fraction
Max sequence gap fraction
Min sequence identity
Max sequence identity
Reference sequence index
Normalization type
Frobenius
Randomization trials
Pseudo-count lambda
Significant eigenmodes
Sector significance cutoff
Reference PDB chain
Reference species search
Truncate to reference positions
MMseqs2 preclustering
Automatic above 50,000 sequences
Precluster sequence identity
Precluster coverage
Precluster coverage mode
0
Initial position gap threshold
Export numeric alignment NPZ
Sequences to retain (1-based)
Similarity sequences to retain (1-based)
Force sequence correlations
Automatic similarity sequence threshold
Similarity sequence sample size
Similarity reference sequence (1-based)
Use MMseqs2 for sequence similarity
Automatic similarity sample cap
Disable automatic similarity subsampling
Retain randomized SCA matrices
Store SCA and sector arrays as float32
Independent components
Automatic eigenmode cap
Export MATLAB workspace
Skip updated database export
Batch pairing
All combinations
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