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Muscle5

Muscle5 documentation topics

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

Trees and bootstrapping
Make a tree with ensemble bootstrap values
Bootstrap values explained
Transfer expectation
Felsenstein confidence

Algorithms
Parallel Perturbed Probcons (PPP) algorithm
Super5 algorithm
Hidden Markov model (HMM)
HMM parameter perturbations
Guide tree permutations