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Fig. 1 | BMC Evolutionary Biology

Fig. 1

From: Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences

Fig. 1

Overview of the four steps of HmmCleaner. a. Creation of a pHMM from the MSA. In the diagram representing the pHMM, squares correspond to main states of the model whereas diamonds are insertion states and circles deletion states. b. Alignment of one envelope of a given sequence of the MSA. c. Computation of the cumulative similarity score based on the analysis of the string of match/mismatch (underlined in yellow) using the four-parameter scoring matrix. d. Determination of low similarity segments as continuous sequence stretches with similarity score < 1 in which at least one position reached a null score

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