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In this case, the authors could easily sort the sequence data due to the unique genetic sequence of each original target.
BAM files containing the sequencing data were sorted using Picard Tools [ 24] SortSam and converted to FastQ format using BamToFastQ program [ 25].
The sequence data obtained was sorted according to their tag sequences and preliminary assembled into seven subsets using the Newbler assembler.
We explicitly modeled incomplete lineage sorting through the use of a multispecies coalescent tree for the sequence data.
We assembled the sequence data for each clade into gene clusters by sorting the sequences with all-against-all BLAST clustering using BLASTCLUST (settings: -L 0.25 -S 75 -b T -p F -e 10E-5 -S 1).
X.L. analyzed the sequencing data.
M.R. generated the sequence data.
Y.G. analysed the sequencing data.
J.C. and L.L. analyzed the sequence data.
Y.G. helped further analyze the sequencing data.
J.C., D.K. and C. Lanz generated the sequencing data.
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