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Fig. S1. Example of an indel distance matrix estimation using the MCIC function.

Fig. S2. Schematic view of the MCIC pairwise indel distance estimation between sequences C and E represented in Figure S1.

Fig. S3. Example of an indel distance matrix estimation using the SIC function.

Fig. S4. Example of an indel distance matrix estimation using the BARRIEL function.

Fig. S5. Example of an indel distance matrix estimation using the FIFTH function.

mee312118-sup-0002-DataS1.fastext/fas42KData S1. Sequence alignment analysed using SIDIER as described in the main text.
mee312118-sup-0003-DataS2.fastext/fas42KData S2. Sequence alignment used as input for the batchfile provided in Data S4.
mee312118-sup-0004-DataS3.rtext/r6KData S3. Commented script to perform a complete sequence analysis using SIDIER.
mee312118-sup-0005-DataS4.rtext/r2KData S4. Batchfile to perform a customized analysis using SIDIER in only 5 steps (see instructions in the first lines of the file).

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