Reference tree size for a marker gene?

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abhijeet singh

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Jan 15, 2019, 3:58:34 PM1/15/19

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Hello,

I was wondeing if someone have an idea about the size of reference tree that pplacer can handle for a marker gene/AA alignment? I have seen the original paper and pplacer have been used with a reference tree of 1600 sequences. Anyone got any idea or practical experience about that?

I have been in contact with an expert in phylogeny and we have seen that a large tree posses some theoretical limitations on the basis principle on which pplacer works.

A discussion over this topic would be appreciated.

/Abhi

siavash mirarab

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Jan 16, 2019, 3:22:12 PM1/16/19

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We were able to consistently run it on 1000 species but not 5000.

https://www.biorxiv.org/content/early/2018/11/23/475566

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