Fig. 2

Impact of open gap penalty value on average pairwise similarity, proportion of pairwise comparison having ≥97.5% genetic similarity and maximal number of gaps introduced per sequence for Clustal W, MAFFT, T-Coffee and Muscle. The different statistics were computed on each aligned dataset. Results obtained for dataset sizes of 238, 476 and 1191 were averaged over 10, 5 and 2 replicates, respectively. Results for the 2383 dataset are shown only for algorithms that generated results in less than two weeks. Recombinants were included in the datasets. Arrows indicate open gap penalty value selected for further analyses. *Default value of open gap penalty as defined by the algorithm user manual