Examples
muscle -resample diversified_ensemble.efa -output resampled_ensemble.efaDescription
The resample command creates a resampled ensemble from an existing ensemble (usually a diversified ensemble).If the output filename has a @, then one FASTA file is generated for each replicate where @ is replaced by the replicate name, e.g. resample.43, otherwise all replicates are written to one EFA file.
Typically, you will want to make one tree from each MSA in the resampled ensemble. To get separate FASTA files suitable for input to tree estimation software, you can use the efa_explode command
See also how to calculate a tree with bootstrap values.
Options
-replicates N
