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Alexey Kozlov edited this page Jan 17, 2019 · 5 revisions

Intro

Before you start:

Checkpointing

RAxML-NG supports checkpoints that means if your run crashes because you have exceeded, for instance, the cluster time of 24 or 48 hours you can just re-start it from where it was stopped by re-invoking the same run with the same run ID. This is very important for analyzing very large datasets.

Start with:

raxml-ng --bootstrap --msa prim.phy --model GTR+G --prefix A1 --seed 2 --threads 2 --bs-trees 100

and interrupt it by pressing CTRL+C after a couple of replicates, then type again:

raxml-ng --bootstrap --msa prim.phy --model GTR+G --prefix A1 --seed 2 --threads 2 --bs-trees 100

and watch the log:

[00:00:00] NOTE: Resuming execution from checkpoint (logLH: -7132.10, ML trees: 0, bootstraps: 22)

:-) If you want to restart the run form scratch for the same run ID, you need to specify --redo.

Terraces

Under the unlinked branch length model, certain patterns of missing data can induce so-called phylogenetic terraces: a phenomenon when multiple topologically distinct trees have exactly identical likelihood scores.

To illustrate terrace detection, we will use the following small alignment:

$ cat terrace.fa

>t1 
AACCG-----
>t2 
AAGGG-----
>t3 
ATTGTCGGGT
>t4 
-----AAGGC
>t5 
-----AATGC

and the corresponding partition file:

$ cat terrace.part

  GTR+G, p1=1-5
  GTR+G, p2=6-10

Let's first do a tree search on that data:

raxml-ng --msa terrace.fa --model terrace.part --tree pars{1} --threads 1 --prefix A2 --brlen unlinked --force

RAxML-NG will automatically check if the best-found ML tree lies on a terrace, and print the corresponding warning:

WARNING: Best-found ML tree lies on a terrace of size: 15

We can also use --terrace command to check if a given user-specified tree resides on a terrace:

raxml-ng --terrace --msa terrace.fa --model terrace.part --tree A2.raxml.bestTree --threads 1 --prefix A3 --brlen unlinked --force

which will yield the following output:

Loading tree from: A2.raxml.bestTree

WARNING: Best-found ML tree lies on a terrace of size: 15

Tree terrace (in compressed Newick format) was saved to: /home/alexey/tutorial/A3.raxml.terrace
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