Inferring a phylogeny

There are multiple way to infer a phylogeny. Here, we will follow a maximum likelihood approach, and use the software raxml-ng.

We will use the following command to infer a quick tree with 100 bootstrap replicates:

raxml-ng --all --msa all_loci.fasta --model GTR+G --prefix tree --threads 2 --seed 2 --bs-metric fbp

We can check whether the topplogies converge with:

raxml-ng --rfdist --tree tree.raxml.mlTrees --prefix RF

And we can check the convergence of the bootstrap with:

raxml-ng --bsconverge --bs-trees tree.raxml.bootstraps --prefix t2 --seed 2 --threads 2 --bs-cutoff 0.01

Don’t forget to check raxml-ng tutorial for more options: https://github.com/amkozlov/raxml-ng/wiki/Tutorial

The file ending in .support shows our phylogeny with bootstrap support. We can open it in FigTree.

You might want to change the label names to species name + accession, instead of only accession. We can do that with phyx, more specifically with pxrlt (taxon relabelling for trees). We will need list of current and new names.

For the current names, we can simply get from out acc file, and the new names we can get from the Nicholls et al. 2015 paper:

I_auristellae_FG113
I_cylindrica_FG35
I_nouragensis_FgIntype
I_cinnamomea_KGD465
Zygia_mediana_Zygia917

pxrlt -t tree.raxml.support -c current -n new > tree.raxml.support.names

Now we have a phylogeny with branch support values and proper label names. Enjoy!