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Nei-Saitouneighbor-joining algorithm for phylogeny construction.
- Python 2.7
- R, Packages - “ape” and “RColorBrewer”
install.packages(c('ape','RColorBrewer'))
python main.py hw3.fna
This generates the following files:
- genetic_distances.txt
- edges.txt
- tree.txt
- bootstrap.txt
All the above files are in the foldersubmission.
For visualization:
Rscript scripts/hw3-plot-newick.r tree.txt hw3-tip-labels.txtRscript scripts/hw3-plot-edges.r edges.txt hw3-tip-labels.txt
For bonus visualization:
Rscript scripts/hw3-plot-edges.r edges.txt hw3-tip-labels.txt bootstrap.txt