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Table 1 A summary of all the methods

From: Bootstrapping phylogenies inferred from rearrangement data

BGN, BGN* Bootstrap by adding Gaussian Noise to the distance matrix.
BPC, BPC* Bootstrap by Pairwise Comparisons: for each pair of sequences/genomes, sample
  columns/adjacencies with replacement to compute distance.
BC, BC* Classical Bootstrap: sample columns with replacement to obtain replicate; sample
  adjacencies with replacement to compute distance matrix.
PJ, PJ* Parsimony Jackknifing: choose each column with 1−1/e probablity to create replicate;
  sample adjacencies with replacement and discard duplicates to compute distance matrix.
dJK, dJK* d%-JackKnife: Omit d% of columns at random to produce replicate; omit d% of adjacencies
  at random to compute distance matrix.
BP, BP* Bootstrap by Perturbations: apply random mutations/rearrangements to get replicates.
JG* Jackknife Genes: Marker based jackknifing method of Shi et al for rearrangement data.