Resampled ensemble of alignments

A resampled ensemble is a set of new MSAs generated an existing ensemble (call it E) by selecting columns at random from MSAs in E, with replacement. "With replacement" means that selecting a column does not delete it, so a given column can be selected any number of times. If the input ensemble has just one MSA, or all MSAs are identical, this is exactly equivalent to the Felsenstein bootstrap which is widely supported by phylogenetic tree software. You don't usually see the ensemble used to calculate Felsenstein bootstrap values because the replicate alignments are calculated internally by phylogenetic tree software and then saved to obscure files or discarded.

A resampled ensemble of alignments is used to create a resampled ensemble of trees.

See also how to calculate a tree with bootstrap values.

References

Felsenstein, J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 422 39, 783-791 (1985). https://doi.org/10.2307/2408678