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Classes Class Description pal.tree.UPGMATree Use ClusterTree
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Methods Method Description pal.datatype.DataType.Utils.isGap(DataType, char) use DataType.isGapChar()pal.distance.DistanceMatrix.getIdGroup() distance matrix now implements IdGrouppal.misc.TimeOrderCharacterData.getIdGroup() TimeOrderCharacterData now implements IdGrouppal.misc.TimeOrderCharacterData.getSampleCount() Use getOrdinalCount()pal.misc.Utils.argmax(int[]) pal.substmodel.RateMatrix.getRelativeRates() try not to use.pal.tree.TreeUtils.getBootstrapSupportByCladeTree(String, Tree, Tree[]) Use getReplicateCladeSupport insteadpal.tree.TreeUtils.scale(Tree, double, int) use getScaled()