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

232 views
Skip to first unread message

Алсу Назипова

unread,
Jul 23, 2019, 5:25:57 AM7/23/19
to IQ-TREE
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

unread,
Jul 23, 2019, 7:42:27 PM7/23/19
to IQ-TREE, Алсу Назипова
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?

--
You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/iqtree/8d9a3852-7a57-4909-87a5-f6028d73f05d%40googlegroups.com.

Алсу Назипова

unread,
Jul 24, 2019, 6:55:12 AM7/24/19
to IQ-TREE
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?

--
You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
To unsubscribe from this group and stop receiving emails from it, send an email to iqt...@googlegroups.com.
Reply all
Reply to author
Forward
0 new messages