1. IQtree ML building tree:

iqtree -s output110 -m GTR+R6

The -s parameter is the result of multiple sequence alignment of the input

-Redo: The IQ-Tree runtime will save the result of each successful run, and the run interrupt will restart from the breakpoint. This is great for large data sets. If you want to start over, add the parameters. -pre: Change the output file name, prefix - MTree: Check all available models -M: Specify the required model GTR+R6 ML maximum likelihood method to construct the evolutionary tree

Output results:
Example. phy. Iqtree records relatively specific evolutionary tree construction information. And information about the optimal alternative model.
Example. phy. treefile records the newick text built into the evolutionary tree, which should be the most important output file
Example.phy.log is mainly used for software author debug.

2. ITOL Visualization

The website: http://itol.embl.de/
Upload the tree file and beautify the build tree.
image.png

Results analysis:
As shown in the figure, the downloaded 100 genome data can be observed to have high sequence similarity with the assembled 11 genomes (highlighted in blue). Sample 3 has the closest similarity to the reference genome.