Fig. 1

Illustrated example of SERES resampling random walk on unaligned sequences. Detailed pseudocode is provided in Additional file 1: Additional methods section: Algorithm 2. a The resampling procedure begins with the estimation of a consensus alignment on the input set of unaligned sequences. b A set of conservative anchors is then obtained using the consensus alignment, and anchor boundaries define a set of barriers (including two trivial barriers—one at the start of the sequences and one at the end of the sequences). c The SERES random walk is conducted on the set of barriers. The walk begins at a random barrier and proceeds in a random direction to the neighboring barrier. The walk reverses with certainty when the trivial start/end barriers are encountered; furthermore, the walk direction can randomly reverse with probability \(\gamma\). As the walk proceeds from barrier to barrier, unaligned sequences are sampled between neighboring barrier pairs. d The resampling procedure terminates when the resampled sequences meet a specified sequence length threshold