Figure 11.

a) If the window borders are indicated by the first and last ancestral Felsenstein wildcard within the window (indicated as underlined), a proposed alignment could lead to a situation from which the original alignment could not be obtained by the same rules. b) If the window borders are indicated by neighbouring ancestral Felsenstein wildcards that are not within the window and will not to be realigned, no possible alignment will lead to such a situation, the original alignment will always be proposed back with a positive probability.

Mikl√≥s et al. BMC Bioinformatics 2008 9:137   doi:10.1186/1471-2105-9-137
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