Figure 2.

Example output from the SeqFIRE indel module. The module produces five different outputs (A–E). The alignment with indel annotation is visualized in Jalview (A) and text mode (B). The indels list is a numbered sequential list of all indels including the location of the indel in the alignment and the full sequence of the indel region for all taxa (C). The simple indel matrix is a NEXUS-formatted matrix with all simple indels scored as 0 or 1 (absence or presence) for all taxa (D). The indel module also outputs an alignment with all indel regions removed, also in NEXUS format (E). Outputs B–E can be downloaded as a single file or separately using links at the top of the output page.