bootstrap - Githubissues

hcsun1 commented 2 years ago

Hello,

How do I get a inferred tree with bootstrap by using ASTRAL-Pro2?

Thank you!

chaoszhang commented 2 years ago

Currently ASTRAL-Pro does not provide bootstrap support but instead provides a localPP support. See https://academic.oup.com/mbe/article/33/7/1654/2579300

hcsun1 commented 2 years ago

How to get a localIPP support by ASTRAL-Pro2? Could you please provide the running command or parameter?

Thank you!

chaoszhang commented 2 years ago

ASTRAL-Pro2 by default outputs a species tree with local PP support. If you are using windows, double click aster-gui.exe in the exe folder and select your input file, (optional) output file name and directory, and number of threads. You will see by default, branch annotation is local PP support. If you are using linux/mac, run make; ~/bin/astral-pro -t 8 -o output_filename.treefile -i all.iqtree.input.nobootstrap.treefile

Edit: If you are using the GUI version, the output tree is not the one printed on the prompt, but in the output file (inferred_species_tree.nw in the current directory by default).

chaoszhang commented 2 years ago

For example, (M_domeMMliu,M_domesMjiu)0.895739:0.026947 means the branch inciding to the common ancestor of M_domeMMliu and M_domesMjiu has localPP support 0.895739.

hcsun1 commented 2 years ago

What is the difference between ../bin/astral-pro and ../bin/astral?

I run ../bin/astral .It can not provide localPP.

hcsun1 commented 2 years ago

And the topological structure of these two results (../bin/astral-pro and ../bin/astral) is not consistent.

chaoszhang commented 2 years ago

astral is not designed for multicopy gene tree. They are two different programs.

hcsun1 @.***>于2022年8月3日周三02:21写道：

What is the difference between ../bin/astral-pro and ../bin/astral?

I run ../bin/astral .It can not provide localPP.

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chaoszhang commented 2 years ago

astral is a reimplementation of ASTRAL-III. See this paper. astral-pro is a reimplementation of ASTRAL-Pro. See this paper.

chaoszhang commented 2 years ago

In astral, when input trees contain duplicated copies, they are treated as two individuals of the same species. See astral-multi.

chaoszhang commented 1 year ago

ASTRAL-Pro2 by default outputs a species tree with local PP support. If you are using windows, double click aster-gui.exe in the exe folder and select your input file, (optional) output file name and directory, and number of threads. You will see by default, branch annotation is local PP support. If you are using linux/mac, run make; ~/bin/astral-pro -t 8 -o output_filename. treefile -i all.iqtree.input.nobootstrap.treefile;

2022年8月2日(火) 6:14 hcsun1 @.***>:

How to get a localIPP support by ASTRAL-Pro2? Could you please provide the running command or parameter?

Thank you!

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chaoszhang / ASTER

bootstrap #7