The hemagglutinin subtypes from Influenza A can be divided into distinct lineages. This is important for tracing the evolutionary history of the gene. It allows regional lineages to be identified and studied. The process of lineage identification depends on phylogenetic analysis to identify the distinct clades within the data. Identification of lineages within the Influenza Internal genes would help to simplify the analysis of reassortment where these genes are transferred between subtypes. In this paper we show that a rapid clustering method can be used to assign lineages to the internal gene segments without the need for a full phylogenetic analysis.