Align sequences to generate MSA or ensemble
align Align sequences using the PPP algorithm
super5 Align large datasets using the Super5 algorithm
Manipulate ensembles
efastats Report miscellaneous information about MSAs
efa_explode Extract FASTA files from EFA file
fa2efa Combine FASTA files into one EFA file
disperse Calculate the dispersion of an ensemble
addconfseq Calculate column confidences
letterconf Calculate letter confidences
maxcc Extract MSA with highest CC
resample Generate resampled ensemble
