mitogenome_tree

Mitogenome phylogenetic tree workflow. This does two things

1. tree_prep.R creates the concatenated alignment and partitionfinder config files (but it won't run partitionfinder or build the trees for you)
2. Once you've run the MrBayes & RAXML analyses, come back here with your consensus trees (in data/output/bayes.tre and data/output/ml.tre) and run plot_tree.R to generate the tree figure used in the paper.

how to run this thing:

• install dependencies
  open R and run renv::restore()
  install mafft however you want, e.g. conda install mafft
  make sure you've got python 3 with BioPython installed, like pip3 install BioPython

  you'll also need an anaconda instance with python 2 to run PartitionFinder, which is easily done:

  $ curl -LO https://repo.anaconda.com/archive/Anaconda2-5.3.1-Linux-x86_64.sh
  $ bash Anaconda2-5.3.1-Linux-x86_64.sh -b -p ~/anaconda
  $ source ~/anaconda/bin/activate
  # do stuff
  $ source ~/anaconda/bin/deactivate

• Replace the contents of data/api_key.txt with a valid NCBI entrez API key

• Run the code in tree_prep.R

• Use the output file partition_finder.cfg to run PartitionFinder 2

  user@computer ~/code/mitogenome_tree $ cd data/partition
  user@computer ~/code/mitogenome_tree $ source ~/anaconda/bin/activate
  user@computer ~/code/mitogenome_tree $ python ~/path/to/PartitionFinder.py .
  .... a bunch of stuff happens ....

• Use data/partitions/analysis/best_models.txt and the output file concatenated_alignment.nex to make your MrBayes nexus file

• Use data/partitions/analysis/best_models.txt and the output file concatenated_alignment.phy to run RAxML.

• Run MrBayes and RAxML

• Copy the output trees to data/output/bayes.tre and data/output/ml.tre and run plot_tree.R

• Now you have the tree plot from the paper