What are the criteria for adjusting q？

[Dream-sugar]

Hello I am very happy have this software can be used in my phylogenetic analysis, but there have some problems I can't fully understand。

1. What are the criterias for adjusting -q？ when I used default 0.05, which cant't delet any species, but when I set it 0.2，it seem to delet species which are long branch compare with other species looked in figtree. 2.What are the output files different compare input files except deletd species and long branch？I thought when abnormally long branches deleted， the topology of some clade will be change, but all of my trees without change except delete long branches. Is it because I didn't find the specific results？

[smirarab]

1. It is hard to set fast and easy rules for -q (corresponding to alpha in the paper). Think of alpha as a threshold for rejecting a null hypothesis. When alpha is set to 0.5, it means that we need very strong evidence that something is abnormal to remove it. This is the default way we have used the method in the past. We have tried to only remove branches that are super long, and clearly long.

Using alpha=0.2 corresponds to removing branches that are somewhat long but not necessarily super long. If you desire that behavior, setting alpha=0.2 is fine.

2. TreeShrink does not compute the updated tree. It gives yous the filtered tree and if you gave alignments, the filtered alignment. You would then rerun whatever tool you used to get the first tree (or even a different tool) on the filtered alignment to get an updated tree. Consider also redoing your alignment because these long branches may reduce accuracy of alignments.

Thanks Siavash

On Thu, Dec 9, 2021 at 10:32 PM Dream-sugar @.***> wrote:

Hello I am very happy have this software can be used in my phylogenetic analysis, but there have some problems I can't fully understand。

1. What are the criterias for adjusting -q？ when I used default 0.05, which cant't delet any species, but when I set it 0.2，it seem to delet species which are long branch compare with other species looked in figtree. 2.What are the output files different compare input files except deletd species and long branch？I thought when abnormally long branches deleted， the topology of some clade will be change, but all of my trees without change except delete long branches. Is it because I didn't find the specific results？

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-- Siavash Mirarab

[Dream-sugar]

Thank you very much for your help and advices!