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Sequence editing and assembly was performed using Geneious 7.1.5 (Biomatters, New Zealand).
SeqScape version 2.0 (Applied Biosystems) software was used for base calling, editing, and assembly of the fragments.
The sequence editing and assembly were done by using BioEdit® Sequence Alignment Editor version 7.0.5.2 (Tom Hall, US).
MJS: editing and assembly of sequencing data, annotation and bioinformatic analyses of the sequence and also writing of the manuscript.
CHEB: bioinformatics analyses and critical revising of the manuscript; JAGS: conception and design of the study and critical revising of the manuscript; ACF: conception and design of the study, editing and assembly of sequencing data, annotation and bioinformatic analyses as well as editing of the manuscript.
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Author's response to 5: All draft reference genome assemblies performed in this study were manually edited and assembly errors were excluded from analysis.
Sequence editing, clustering and assembly analysis resulted in 6,404 unigenes (1,590 contigs and 4,814 singletons).
Sequence editing and contig assembly were performed using Sequencher v4.1.4 (Gene Codes Corporation) or SeqScape v2.5 (Applied Biosystems) and HXB2 as a reference.
Pherogram editing and contig assembly was done manually.
Quality checks, editing and sequence assembly were performed with Geneious v6.1 [ 66].
BES of fingerprinted clones facilitated manual editing and contig assembly validation.
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