Compositions and methods for tracking combinations of mutations in populations by coupling DNA assembly and paired-end sequencing technology with high-throughput sequencing. This allows for an unlimited number of mutation sites in a population of microorganisms to be identified, and allows sites to be sequenced across several replicates. Unique identifiers (DNA bar-codes) can be used to measure fitness data by sequencing of the barcodes multiplexed with the mutation sites with high-throughput short sequencing read technology, allowing selections to be rapidly performed on populations of known combinatorial genotypes.
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