Which number of replicates for UltraFast bootstrap support I have to use to publish my tree in journal?

[Алсу Назипова]

Hi! I don't know which number of replicates  for UltraFast bootstrap support I have to use to publish my tree in journal. I reed the paper about Ultarfast but authors reccomend minimal number 1000.

I know for standart bootstrap number is 1000 for publication in journal althrou 100 is the minimal number. Can I use 10000 for ultrafast?

[Minh Bui]

Hi,

The ultrafast bootstrap replicates should be at least 1000 (actually IQ-TREE does not allow you to specify lower number). For long (multi-gene) alignments, I’d actually recommend to use more replicates, which does not affect the runtimes subtantially (i.e. going from 1000 to 10000 does not increase the runtime 10-fold, but only 2x or so). 

For partition models I’d also suggest to use GENE resampling or better GENESITE resampling. See our UFBoot2 paper for the reason behind it (https://doi.org/10.1093/molbev/msx281).

Cheers,

Minh

On 23 Jul 2019, at 7:25 pm, Алсу Назипова <sushe...@gmail.com> wrote:

Hi! I don't know which number of replicates  for UltraFast bootstrap support I have to use to publish my tree in journal. I reed the paper about Ultarfast but authors reccomend minimal number 1000.

I know for standart bootstrap number is 1000 for publication in journal althrou 100 is the minimal number. Can I use 10000 for ultrafast?

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[Алсу Назипова]

Thank you very much!

среда, 24 июля 2019 г., 2:42:27 UTC+3 пользователь Minh Bui написал:

Hi,

The ultrafast bootstrap replicates should be at least 1000 (actually IQ-TREE does not allow you to specify lower number). For long (multi-gene) alignments, I’d actually recommend to use more replicates, which does not affect the runtimes subtantially (i.e. going from 1000 to 10000 does not increase the runtime 10-fold, but only 2x or so). 

For partition models I’d also suggest to use GENE resampling or better GENESITE resampling. See our UFBoot2 paper for the reason behind it (https://doi.org/10.1093/molbev/msx281).

Cheers,

Minh

On 23 Jul 2019, at 7:25 pm, Алсу Назипова <sushe...@gmail.com> wrote:

Hi! I don't know which number of replicates  for UltraFast bootstrap support I have to use to publish my tree in journal. I reed the paper about Ultarfast but authors reccomend minimal number 1000.

I know for standart bootstrap number is 1000 for publication in journal althrou 100 is the minimal number. Can I use 10000 for ultrafast?

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