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A flat-embedding procedure was used after which each tissue block was trimmed using a single-edged razor blade under a dissecting microscope.
Full alignments were trimmed using G-blocks [ 123] and were run through ProtTest using the default settings to determine the optimum evolutionary model for phylogenetic analyses [ 124].
The alignments were trimmed using GBlocks (Castresana, 2000 ), allowing for smaller final blocks, gap positions within the final blocks, and less strict flanking positions.
Vector sequences were trimmed using Cross_Match.
Subsequently, vector sequences were trimmed using Crossmatch.
Illumina reads were trimmed using Trimmomatic [ 20].
Vector sequences were trimmed using Cross-match.
IT ESTs were trimmed using TIGR SeqClean software.
Any sample reads that required trimming for quality were trimmed using BWA during the alignment process.
The Illumina reads were trimmed using Trimmomatic [ 79].
Low quality reads were trimmed using perl script.
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