qiime alignment mafft error

[Sue (Fletcher)]

Hello,
I have the same issue as described in this post: ERROR: Qiime 2 alignment mafft

My question is: can I use the --p-parttree parameter even when the number of sequences being aligned is less than 1,000,000?

I want to automate the process and avoid having to manually enable or disable this parameter each time.

thank you in advance

[SoilRotifer (Mike Robeson)]

Hi @Sue,

I think you should be fine, as the MAFFT manual suggests that you can optionally use --p-parttree parameter above 10,000 sequences. However, --p-parttree parameter is required for anything above 1,000,000 sequences.

I think you should be generally fine just setting this, assuming you have at least a few thousand sequences. Not sure how well this would work with less than that though...

You can read more about the PartTree algorithm.

-Mike

[Sue (Fletcher)]

@SoilRotifer

Hi @Sue,

I think you should be fine, as the manual suggests that you can optionally use this parameter above 10,000 sequences. However, --p-parttree parameter is required for anything above 1,000,000 sequences.

I think you should be generally fine just setting this, assuming you have at least a few thousand sequences. Not sure how well this would work with less than that though...

You can read more about the PartTree algorithm.

-Mike

I will allow the use of this parameter by default in this case.
thank you very much !!