From alignments to concordance factors

This site covers the steps of the TICR pipeline to go from a bunch of multiple alignments (aligned gene sequences, or loci) to a concordance factors. These concordance factors can then be used to estimate a phylogenetic network that displays the relationships between the species in the alignments.

• The original TICR pipeline

  • analyze each locus with MrBayes
  • do a concordance analysis with BUCKy on each set of 4 taxa
  • summarize all quartet concordance factors (CFs)
  • estimate a species tree using Quartet MaxCut

  Or an alternative pipeline to

  • analyze each locus with RAxML, including bootstrap
  • estimate a species tree with ASTRAL

• TICR test in the R package phylolm (Testing Incongruence Checking in R), also now in Julia in QuartetNetworkGoodnessFit.jl

  • test if a population tree with the coalescent (ILS only) is adequate to explain the quartet concordance factors
  • identify taxa involved in outlier quartets

Topics covered

• Example data
• Gene trees with MrBayes
• Quartet CFs with BUCKy
• Species tree with QMC
• Alternative pipeline: RAxML+ASTRAL
• TICR goodness-of-fit test: is a population tree with ILS sufficient (vs network)?

All these sections are covering the original TICR pipeline well suited for a machine or a cluster of machines without a job scheduler. The scripts automatically parallelize the work across the available cores. Users with access to job schedulers like SLURM or SGE should check the section on SLURM pipeline. The job scheduler does the work of parallelizing the work across available cores. The scripts, in this second pipeline, were created to take full advantage of job scheduler capabilities. They were developed for a cluster running SLURM. Adjustments to the submit scripts will be needed, to adapt to your own SLURM configuration or to the syntax that your job scheduler wants.

Set-up

Locally

• Download BUCKy
• Download QMC
• Download MrBayes
• Git clone this repository: git clone https://github.com/JuliaPhylo/PhyloUtilities.git

For MBL workshop

Login to your particular virtual machine (VM) using the IP address on the sticker attached to the back of your name tag. If, for example, your IP address was 123.456.789.321, you would type the following into the terminal on your local computer (i.e. your laptop) and press the enter key:

ssh moleuser@123.456.789.321

After login, you want to copy the phylo-networks in your home directory:

cp -r moledata/phylo-networks ./
cd phylo-networks

We will not cover an alternative RAxML+ASTRAL pipeline (which you could cover outside the workshop).