Getting started
About Muscle v5
Download and install
Making alignments and ensembles
Commands
Alignments and ensembles
EFA file format
MSA ensemble
Dispersion predicts error rate
Diversified ensemble
Stratified ensemble
Resampled ensemble
Cluster ensemble
Gene subset ensemble
Column and letter confidence
Column confidence (CC)
Letter confidence (LC)
Jalview features
Algorithms
Parallel Perturbed Probcons (PPP) algorithm
Super5 algorithm
Hidden Markov model (HMM)
HMM parameter perturbations
Guide tree permutations