Dear knowledgeable researchers, I'm currently pursuing an undergraduate degree and as a result I do not have so much knowledge in this topic. I'm having som troubles understanding my phylogenetic three construction.
For the construction of a phylogenetic tree UGENE was used. 11 homologous proteins from different species in the same genus/phyla were aligned. For the tree construction PHYLYP Neighbour Joining (NJ) with the distance matrix model “Jones-Taylor-Thornton” was used. Two trees were constructed, one without bootstrapping and one with bootstrapping (1000 pseudoreplicates).
How do I interpret my values? Are they unusable since I have low bootstrap-values in a lot of my nodes? All guidance is appreciated, thank you.
Both trees are drawn as cladograpms with meaningless branch lengths. But in the WithoutBootstrap tree the branch lengths are written below each branch. So we can see there are a few very long branches of 0.2 to 0.3 distance and many short branches with distances of 0.011, 0.052 etc...
When you have a long branch out to a clade that is highly related to each other such as the 0.204 branch out to 3 KFJ sequences, which are each 99% identical to each other, you of course get good bootstrap support for those 3 sequences being in the same clade.
With all the sequence names being the same, other than accession number, it is difficult to see whether KJF sequences are from highly related species, or if they are from different species. If they are from different species it may indicate that the gene has travelled between species on a plasmid or phage.
The lowest bootstrap support is for SUV5 being with WP_029 or going with a group including ETY7, and this is because that branch of 0.08 length is very tiny.
If you use a program such as FigTree to draw the trees, you can draw them with branch lengths proportional to distance, and it is much easier to understand what is going on.
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