/phylogenetic-tree-using-fracminhash

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

Robensen-Folds distance

Add more bacterial genomes Start with a known Phylo tree based off of 16S GTDB te start korbo??

copy, WABI format

check bootstrapping values. sample dist matrix a lot of times. each time see if tree branches change or not