![]() ![]() The lines are moving averages based on an overlapping sliding window of 250 consecutive points.Īlthough numerous studies have demonstrated the theoretical and empirical importance of treating gaps as insertion/deletion (indel) events in phylogenetic analyses, the standard approach to maximum likelihood (ML) analysis employed in the vast majority of empirical studies codes gaps as nucleotides of unknown identity ("missing data"). Many points may be superimposed upon one another, particularly when the y-axis value = 0 (cases where no differences were observed). For the (POY HA dist − POY TA dist ) data points, positive values on the y-axis are cases where the POY TA-reconstructed trees were more accurate than the POY HAreconstructed trees, and the opposite is true for negative values. For the (Clustal HA dist − POY HA dist ) data points, negative values on the y-axis are cases where Clustal HA reconstructions were more topologically accurate than the POY HA reconstructions, and the opposite is true for positive values. ![]() Points to the far right are the most accurate alignments while points to the left are the least accurate alignments. Relationship of POY TAA (total alignment accuracy measured from implied alignments results follow similar pattern shifted to the right if Clustal TAA are used) and the relative performance of topological accuracy of Clustal versus POY for all cases of varying tree shapes and conditions. ![]()
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