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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.

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mahmudhera/phylogenetic-tree-using-fracminhash

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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

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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.

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