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This contains the minimal necessary codes to reproduce the results from the manuscript "Invariant non-equilibrium promoter switching dynamics optimizes information flow in eukaryotes".

Building a multiple sequence alignment well-suited for phylogenetic analysis from read mapping data

Minimum Spanning Tree-based clustering

Assembling SSU

Data analysis related to the manuscript: Harnessing Diversity Generating Retroelements for in vivo targeted hyper-mutagenesis

Display the colormap over the image using an overlay.

Building a supermatrix of characters from a set of multiple sequence alignments