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Fig. 1 | Algorithms for Molecular Biology

Fig. 1

From: Split-inducing indels in phylogenomic analysis

Fig. 1

Non-trivial example of the determination of splids with size \(\ge\) 2 from two concatenated alignments (A and B). Alignment A contains sequence data for all taxa, whereas B lacks sequence information for taxon g. At first, all indel loci are determined (I–IV). Second, indel loci are searched for indels constituting splids. From locus I only indels (4) and (6) fulfill this criterion. Indels (1) and (3) do not share a common 5’ end. Indel (8) is too short. Indels (9) and (10) of locus III are overlapping splids. Whether or not indel (11) is included in the final splid set depends on the applied algorithm. In strict mode it is not included, due to the single-residue indel (13). In fuzzy mode, it is included and taxon g is marked as missing data (“?”) in the binary presence/absence coding

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