/phylogenetic-tree-using-fracminhash

This repo can be thought of as a counterpart to Mashtree - which computes a tree based off of Mash distance. Instead, in this repo, we build a tree based off of FracMinHash distance.

Primary LanguageRoff

Phylogenetic tree using FracMinHash

In this experiment, we will compute pairwise distance using FMH, and then use the distance matrix to compute Phylogenetic tree.

Steps:

  1. Create folder for genomes
  2. Create a file : list of genomes. Line1: name, line2: folder path
  3. Write code that will Open all genomes Then, construct fmh sketches for a bunch of different seeds (1 - 100)
  4. After these, write code that will read genome list, seeds, and output pairwise distances using fmh

#Tree building method that takes into consideration uncertainties #Look into bootstrapping techniques