Creating Phylogenetic Trees (a Happy Ending)

You may remember that I posted a few weeks ago about how to create phylogenetic trees out of similar genes using seaview and RaxML. To re-cap briefly, I created a multiple sequence alignment from FastA files, removed all the gaps so that only the substitutions were left, and then ran it through RaxML to produce the trees. Unfortunately, I couldn’t get the trees to open with treeview.

I spoke to an expert the next day and discovered that treeview has certain dependencies on Ubuntu that were difficult to resolve, so the answer was… to use Windows. I have to admit, it seems like a pretty funny answer to the question, given how much better Ubuntu is for bioinformatics tasks than Windows. Even BioLinux, the Linux built especially for bioinformatics, was unable to open my phylogenetic tree.

Anyway, here are two different views of the same tree for you to enjoy, with highlighting and legends added in MS Paint.

Advertisements

Creating Phylogenetic Trees

Our assignment for the past week has been to create phylogenetic trees from multiple sequences alignments based on clusters of orthologous genes (COGs). Specifically, to decide why a simple BLAST search was unable to accurately place a subject gene from Cryptosporidium parvum into a COG category.

I think this assignment is an interesting exercise in ‘real’ bioinformatics: where data is messy, the programs are challenging to install and use, and in the end you’re not quite sure what you ended up with, but it’s enormous fun anyway!

Read More »