Default amount of ML searches when using the -f a option

[Allison Fuiten]

Hi!

I have, hopefully, a pretty quick & simple question.

I am using the rapid bootstrapping option (-f a) when I'm using RAxML with the following command:

raxmlHPC-PTHREADS -s 032316_partition_aln.fasta -n 032316a_uce -m GTRGAMMA -T 10 -p 1986 -# 1000 -x 1986 -f a -q 032316_partitions.txt

I thought that this will result in 1000 rapid Bootstrap searches based on the -# flag and 20 ML searches by default, but the RAxML_info file seems to indicate that it only does 10 ML searches. Am I misinterpreting the RAxML.info file or is 10 ML searches the default? How would I specify 20 ML searches under the -f a flag setting?


If you could clarify this for me, I would really appreciate it!

Thank you,

Allison

[Fidel Botero]

Hello Allison,

You can find the answer in Fig 2 of the paper describing the fast boostraping (see link below). Long story short, a fast ML search is first conducted starting on every 5th tree of the bootstrapped ones, and the best 10 results are kept to perform a slow ML search.

http://sysbio.oxfordjournals.org/content/57/5/758.full.pdf+html

Cheers,

Fidel

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Fidel Botero-Castro

[Allison Fuiten]

Hi Fidel!

Thank you so much. Figure 2 totally cleared things up for me.

Cheers,

Allison