Computational protocol: Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants

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Protocol publication

[…] The phylogenetic tree was constructed using the MEGA 6.0 software with Neighbor Joining Method with 1000 bootstrap replications. The model used was Jukes Cantor that had the highest log-likelihood score according to the J-model Test (https://code.google.com/p/jmodeltest2/). For the J-model test the precursor alignment was given as the input in “.aln” format. It calculates for the variations in the nucleotide sequences and gives the log-likelihood scores for all the models for phylogenetic tree construction. […]

Pipeline specifications

Software tools MEGA, jModelTest
Application Phylogenetics
Organisms Arabidopsis thaliana, Nicotiana tabacum