pplacer with qiime2

[Huda_Ghori]

Hi

I want to place my sequences on to a reference tree using pplacer. I have never used it before. How can I use it with QIIME2. What file should be used as input to pplacer.

If there is any other program that can help me place my sequences on a reference tree?

Please help

Thanks

[thermokarst]

Hi @Huda_Ghori!

@Huda_Ghori

How can I use it with QIIME2

With the q2-fragment-insertion plugin!

https://docs.qiime2.org/2020.6/plugins/available/fragment-insertion/

Check out this tutorial for an example of how to use it:

https://docs.qiime2.org/2020.6/tutorials/pd-mice/

[Huda_Ghori]

Hi

Thanks, But this method doesnot place my sequences onto the tree which has names of all the species.

I am looking for something that can place my sequences on a reference tree and then I can edit it in iTOL.

[thermokarst]

@Huda_Ghori

I am looking for something that can place my sequences on a reference tree and then I can edit it in iTOL

q2-fragment-insertion will produce just such an Artifact.

@Huda_Ghori

But this method doesnot place my sequences onto the tree which has names of all the species.

I'm not sure I follow - can you please elaborate?

[Huda_Ghori]

Hi @thermokarst

Sorry for being vague. I got it now!

Thanks for the help