Chapter 8 Building Trees

8.1 Background on tree building

Watch the following videos on phylogenetic tree construction

  • Video 1: review
  • Video 2: Tree building (UPGMA)
  • Video 6: Tree building (NJ)
  • Video 5: Tree building (parsimony)

Don’t worry about the details - I just want you to get a sense of different methods of tree building rather than viewing this process as a “black box” where you just put your data into a computer program and get an answer. For a summary read A brief guide to the different methods of phylogenetic tree construction

8.2 Building trees from your data

8.2.1 Likelihood

We’ll take two different approaches to build phylogenies from your data. First, we’ll use software that calculates the likelihood that the data fit the phylogeny. The software will try lots of different phylogenies and pick the case where the data are most likely. When the software runs it will also try resampling the data to see how much support we have for each relationship we estimate.

  • Use nano to open runRAxML.sh in the slurm_submissions folder.
  • Change all lines marked CHANGE
    • The path to the alignment file should be the full path with all folder names to one of the files labeled alignment_pi_m1_nogap.phylip-relaxed (yours may have a different number after m)
  • Submit the script as a slurm job.

8.3 Visualizing trees

8.3.1 Download your results to your computer

  • Check that a file starting with RAxML_bipartitions is in your scripts folder by listing files (i.e. in the same location from which you submitted your scripts).
  • Determine the path to your tree file using pwd.

8.3.1.1 On a Mac

  • Make a new terminal window (use ctrl-t). You are currently on you local computer.
  • cd to a local folder (on your computer - this is not Andromeda) where you will work on this project (make a new folder if you need to)
  • type scp username@ssh3.hac.uri.edu:path/filename . (replacing username with your username, path with the path to your folder as identified in the prior step, and filename with the name of the output from raxml, which should start with RAxML_bipartitions)

8.3.1.2 On a PC

See Transfering Data on URI’s HPC Instructions.

*Navigate to the root folder (/) then into the folder containing your RAxML output

8.3.2 Visualize your tree

  • Download the visualization program FigTree
  • Open your tree file
  • Select the branch leading to your outgroup and click Reroot
  • On the left menu select Node Labels - Display - label and adjust the font size
  • Select Tip Labels and adjust the font size
  • When you have an aesthetically pleasing tree: File - Export PDF

8.4 What does my tree mean?

https://artic.network/how-to-read-a-tree.html

8.5 Other tree building methods

Another method for building phylogenies relies on selecting four species, and determining the relationships of these species based on examining different patterns of sites. Four species are much easier to work with than more as there are only three possible ways these species can be related. We can look at how often the grouping of sites matches each hypotheized why species are related. You can read the full explanation (with visuals) but don’t worry if it’s complicated. This method is implemented in SVDQuartets.

  • Change the necessary files and information in runSVDQ.sh, which is in the slurm_submissions folder, and submit it.
  • Download and examine your results using the same process as for the RAxML tree but noting that you are looking for a file ending in .tre in the folder containing your input alignment.

8.6 Alternative methods of support

The bootstrap approach automatically implemented by RAxML is one method of determining support. However, bootstrap resampling can have limitations when using larger datasets. An alternative approach is to examine the proportion of sites that support each alternative hypothesis given a tree, similar to the SVDQ approach. You can calculate SCF support by editing the runSCF.sh script and inputting your tree from either RAxML or SVDQ and your alignment. If you estimated different trees using the above methods you may try more than one.