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The haplotype alignment was used in evolutionary analyses.
Additional file 2: Character states used in evolutionary analyses and respective citation sources.
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MLST data have been used in evolutionary and population analyses that estimate recombination and mutation rates and also in the investigation of evolutionary relationships among bacteria classified within the same genus [ 8].
Character data that are suitable for use in evolutionary analyses are processed in order to group sampled individuals into natural biological entities.
The ML trees were used in molecular evolutionary analyses to test for change in constraint on lineages leading to Cuscuta nitida and Epifagus.
These ligands and other previously identified ligands used in the evolutionary analyses are shown in Table 1.
Three clones of each Gypsy and Micropia PCR fragments were sequenced and used in the evolutionary analyses.
Moreover, PAGAN-generated alignments of noisy next-generation sequencing (NGS) sequences are accurate enough for the use of RNA-seq data in evolutionary analyses.
For these reasons, we chose to use parsimony which is also the method of choice in evolutionary analyses when large and disparate datasets are involved.
ORF included in evolutionary analyses.
MEGA5 was used for evolutionary analyses (Tamura et al. 2011).
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