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These two topologies have approximately equal likelihood values in each of the totalml and concatenated alignment analyses, although the ML tree in concatenated alignment analysis is the second best tree in totalml analysis, and vice versa.
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Multiple alignment analysis was performed using Multalin (http://multalin.toulouse.inra.fr/).inra.fr/
Multiple sequence alignment analysis was performed using software CLUSTAL × 1.8.
Subsequently, multiple alignment analysis was performed with DNAMAN 6.0 software.
Similar nucmer alignment analysis was also carried out for the sequence generated for the same gene on the resequencing array platform and the reference sequence.
Multiple alignment analysis was performed with ClustalX.
Protein sequence alignment analysis was viewed through Jalview program [ 27].
A multiple alignment analysis was carried out on AP2 domain sequences from Hevea, Arabidopsis and Populus.
Multiple alignment analysis was performed on full-length AP2 domain sequences from Hevea, Arabidopsis and Populus.
Multiple sequence alignment analysis was performed using CLUSTAL W (1.83) (http://sbcr.bii.a-star.edu.sg/clustalw/).sg/clustalw/
The sequence databases used for alignment analysis were obtained from NCBI.
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