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The most-parsimonious trees of the complete mtDNA sequences were reconstructed manually and verified by means of the Network 4.5.1.0 program (www.fluxus-engineering.com), and using mtPhyl program (http://eltsov.org), which is designed to reconstruct maximum parsimony phylogenetic trees.
Afterward, they can be filtered manually and verified in the laboratory.
A mtDNA COI haplotype network for H. armigera was constructed manually and verified using the program TCS, version 1.13 [ 59].
The initial alignment was adjusted manually and verified using Harmony3 (J. Shi, unpublished), which matches observed substitution frequency in the alignment with predicted substitution frequency from standard and environment specific substitution tables.
The most-parsimonious trees of the complete mtDNA sequences were reconstructed manually, and verified by means of the Network 4.5.1.0 software [ 52], and using mtPhyl software (http://eltsov.org), which is designed to reconstruct maximum parsimony phylogenetic trees.
Amino acid sequences were aligned with those inferred from previously characterised mt genomes for species of Strongylida (i.e., An. duodenale, Ne. americanus and Co. oncophora) and C. elegans using Clustal W [ 57], adjusted manually and verified using BioEdit v.7.0.3 [ 58].
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If an error is detected, the program or the model is manually modified and verified again.
Since the attenuation maps were not measured directly from the PET/MRI scanner at the time of PET imaging, they had to be manually registered and verified to the PET volumes in order to incorporate into offline reconstruction.
Given our purpose to model a co-authorship network using a small subset of papers, we manually reviewed and verified each of the 72 highly cited network papers in the WoS database to identify any ambiguities.
Some tracks were manually examined and verified.
The corresponding formal context was manually created and verified by the NetWellness experts.
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