Hello, I am new microbiology researcher currently researching bacteria using whole genome sequencing and currently doing analysis. I intend to create bacteria phylogenetic tree using BV-BRC services. The tree was succesfully created using MAFFT program with 1000 single copy gene settings. I tried creating the tree by including other bacteria with different species but same genus and without including it. The question is :
- Is the "different species but same genus" bacteria can be categorized as outgroup? How can I determine an outgroup for a particular tree?
- Is outgroup necessary for creating a phylogenetic tree? I'm more familiar to rooted phylogenetic tree so, can I create a rooted tree without including an outgroup?
- I intend to observe the relationship between isolate and correlate it with its sequence type. Which tree is the most valid tree in this case?
Here I attached picture containing both tree using and not using other species bacteria. Note the isolate is labeled using number, the same number before a full stop means the same species of bacteria. All of the isolate is within the same genus.
Thank you for your help and suggestion. :)
(First picture : Only containing 1 species of bacteria)
(Second picture : Including other species bacteria but still within the same genus)
