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deena-b edited this page Jun 27, 2019 · 4 revisions

Determine cell lineage relationships w/ machine learning

Aim: use machine learning to create a dendogram that shows mitochondria sequence similarity between cells

Data

Input: 1 fasta file per cell

Methods

Calculate a sequence similarity matrix

how?

Perform heirarchical clustering

scikitlearn dendogram (or R h-clust)
- principal component analysis?
  - See Serge's: phylogenetic tree and distributed genome represenation.ipynb

Generate a cluster heatmap

seaborn (See Serge's ipynb, link above)

Google these terms or read these pages to find out more about methods we should consider

boosted decision tree
Markov chain Monte Carlo (MCMC)
- How would you explain Markov Chain Monte Carlo (MCMC) to a layperson?
Bayesian Evolutionary Analysis with BEAST (Book)
hamming distance
Andrew Rambaut
- http://tree.bio.ed.ac.uk/
- http://tree.bio.ed.ac.uk/software/beast/
Beast
- https://beast.community/
Beast2
- https://www.beast2.org/
- https://www.beast2.org/glossary/

Download Practice Fasta Files

Flu genes are short and there are tons of them. For an example on how to download ~100 fasta files that are ~1,500 nucleotides (nt) long, see our tutorial "dwnld flu fa"