Abstract: The invention relates to identification of individual nucleic acid sequences from a mixed nucleic acid population. A typical application is to determine the bacteria present in sample containing a mix of several different bacteria. Present techniques require initial cultivation of the mixed bacteria sample and manual separation of the bacteria prior to sequencing. The invention allows for identification of the different bacteria by direct sequencing of the mixed bacteria sample without prior cultivation and separation. One aspect of the invention relates to generating a degenerate sequence from a chromatogram obtained by sequencing a mixed bacteria sample. Another aspect relates to base-calling, i.e. identification of individual sequences making up the degenerate sequence from the mixed bacteria sample. In this aspect, the degenerate sequence is divided into degenerate subsequences from which query subsequence combinations are generated.