Fig. 3From: Optimization of sequence alignments according to the number of sequences vs. number of sites trade-offORTHOMAM trade-off curves. Proportion of site gains (final number of sites - initial number of sites, divided by the final number of sites) as a function of the proportion of sequences removed. Points show the median over the 11,305 gene families, and shaded areas show the first (25 %) and third (75 %) quartiles. Three methods are superimposed: hierarchical clustering of sequences using the overlap distance and median linkage, the fasttree maximum likelihood tree reconstruction, and a fixed tree representing the known phylogeny of speciesBack to article page