anicksaha / neighbor_joining

Nei-Saitou neighbor-joining algorithm for phylogeny construction/inference. Neighbor joining is a bottom-up (agglomerative) clustering method for the creation of phylogenetic/evolutionary trees.

Neighbor joining

Nei-Saitou neighbor-joining algorithm for phylogeny construction.

Prereq:

• Python 2.7
• R, Packages - “ape” and “RColorBrewer”
• install.packages(c('ape','RColorBrewer'))

How to Run?

• python main.py hw3.fna

This generates the following files:

1. genetic_distances.txt
2. edges.txt
3. tree.txt
4. bootstrap.txt

All the above files are in the folder submission.

Visualize

For visualization:

• Rscript scripts/hw3-plot-newick.r tree.txt hw3-tip-labels.txt
• Rscript 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