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: .. code-block:: bash 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: .. code-block:: bash raxml-ng --rfdist --tree tree.raxml.mlTrees --prefix RF And we can check the convergence of the bootstrap with: .. code-block:: bash 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: ``_ 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: .. code-block:: bash I_auristellae_FG113 I_cylindrica_FG35 I_nouragensis_FgIntype I_cinnamomea_KGD465 Zygia_mediana_Zygia917 .. code-block:: bash 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!