mafft or fragment-insertion

[SoilRotifer (Mike Robeson)]

Yeah, like I said:

@SoilRotifer

I typically run both de novo and fragment insertion approaches on my data. Sometimes they are quite different, other times they are not. I try to stick with fragment-insertion when possible

In this case, these plots look identical, just flipped on Axis 2. ProTip: you can invert any of the axes in the visualizer. In this case I'd invert Axis 2 to make it look more like the other PCoA plot. Also, this brings up another point: if your biological signal is very robust, it will not matter if you use de novo or fragment insertion output. So, pick your favorite . Seems like the variance along the axes is is better explained with the fragment insertion.