Computational protocol: Real time monitoring of PtaHMGB activity in poplar transactivation assays

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Protocol publication

[…] The phylogenomic comparison among the different 5′ cis regulatory sequences were done using mVISTA online application [].We used protein sequences to do phylogenetic trees. We used MUSCLE algorithm to do the alignments (200 iterations) and neighbour-joining, UPGMA and maximum likelihood to infer the tree. To carry out this work we used MEGA7 application []. […]

Pipeline specifications

Software tools mVISTA, MEGA
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Populus tremula