Scripts relating to the phylogenetic analysis of Arabidopsis centromeric sequences, for the purposes of Materials and Methods.
For visualistion of repeat sequences, see: 'Initial Visualisation of Repeat Lengths.ipynb'
For scripts exploring the best way to prepare the data, see: 'Analysis of Col-0 BLASTALL by Chromosome and Filtering.ipynb' 'General FASTA file generator.ipynb' 'BLASTCLUST Analysis.ipynb'
For scripts that generate FASTA files for use in mafft alignment, and later tree building, see: 'General FASTA file generator.ipynb' 'FASTA generator by chromosome.ipynb' 'Mega-tree FASTA file generator.ipynb' 'Col-0 Epigenetic and Structural data FASTA file generator.ipynb'
For scripts visualising Epigenetic and Structural Rearrangment data, see: 'Analysis of Epigenetic Data and Strucutral Arrangment Data for Col-0.ipynb'
For scripts visualising percentage identity of sequences, see: 't2t clustal.ipynb'
For scripts running mafft and iqtree, see: 'Run_tree__t2t180.sh' 'Run_tree__mega2.sh'
For scripts annotating and visualising trees, see: tree_visualisation.py