By Peter Unmack

First you have to establish an account on CIPRES. You can register here.

Follow my instructions on running GARLI here so that you know how to properly setup your configuration files.

I find it much easier to use my own conf file than to use the tool on CIPRES for creating one, thus this is written for using your own file.

In your own conf file change the following

datafname = infile

If using a starting tree comment out [attachmentspertaxon = XX] and set

streefname = starting.txt

For a standard ML tree search use the following settings in the conf file

searchreps = 10 (but read below first)

bootstrapreps = 0

For bootstrapping use use searchreps = 1 and bootstrapreps = 1.

You set the number of replicates you wish to run in the CIPRES interface as per instructions below.

Setting parameters to run GARLI on CIPRES

In CIPRES tick the second and forth box stating you are using your own conf file.

Set the amount of memory in your conf file (lowest value is 2000)

Select the conf file (it helps to name your conf files uniquely before you upload them to CIPRES).

Tick the box for “I have set the values of searchreps and bootstrapreps correctly”

There are two ways to search for the best ML tree on CIPRES. When run with searchreps = 10 (in the conf file) GARLI will tell you which tree had the best score and whether they had the same topology or not from each independant run. When run as per instructed on the CIPRES webpage (searchreps = 1 in the conf file) you won't get the topology comparison, only which tree had the best score. To obtain the topology comparison I set searchreps = 10. In the conf file and in the CIPRES interface I set searchreps = 2 (you can't set it to 1) and bootstrapreps = 0 in the interface. That does two independant runs, which is double what you need, but it gives the toplogy comparison. Alternatively, set searchreps = 1 in the conf file and set searchreps = 10 in the CIPRES interface and examine the garli_scores.txt file to find out which run had the best score, but you will have to find another way to compare their topology.

For a bootstrap analysis specify searchreps = 1 and bootstrapreps = 1 in the conf file. In the CIPRES interface set searchreps = 1 and bootstrapreps = 250 (or whatever value you wish to obtain). All the trees will be combined into a file called allBootTrees.tre.

Select the name of your constraint file if using one.

When you downoload your results scroll to the bottom of the list as most of the key files you need will be placed there.

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