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The resulting alignments were filtered for uniquely aligned reads, and realigned using GATK v.2.3-9-ge5ebf34.
Their sequences were aligned using MUSCLE [ 100] and the resulting alignments were concatenated.
Raw sequence data were aligned with the Staden Package [ 48] and the resulting alignments were manually corrected.
Sequences were aligned to corresponding HMM by using HMMALIGN and the resulting alignments were analyzed by RNAz (version 0.1.1) [ 37].
Sequences were aligned using Clustal X [59], followed by manual editing of the resulting alignments.
Secondly, we used different short-read aligners to remap the reads and ran MaSC on the resulting alignments.
Estimated recombinants in the resulting alignments of the total haplotypes were 5.04% (Table 2).
The resulting alignments were displayed with Jalview [43].
The resulting alignments were used for phylogenetic analysis.
The resulting alignments were inspected and ambiguous areas were removed before phylogenetic analyses.
The resulting alignments were manually modified using BioEdit program (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).html
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