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chaoszhang / ASTER

Accurate Species Tree EstimatoR: a family of optimation algorithms for species tree inference (including ASTRAL & CASTER)
GNU Affero General Public License v3.0
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terminal branch is too long sometimes #26

Closed XiaoTW123 closed 5 months ago

XiaoTW123 commented 5 months ago

Hi, prof. Zhang, I inferred the weighted species tree using astral-hybrid, however, I found that sometimes few terminal branches were twice longer than the other species. Could you please tell me what causes this phenomenon? image

chaoszhang commented 5 months ago

Terminal branch lengths are meaningless in wastral and internal branch lengths are in coalescent units which you may have a hard time interpreting. You got this phenomenon because that such branch was the root and figtree arbitrarily gave it branch length 2 instead of 1. However, you can correctly compute all branch lengths in mutation units (similar to IQTREE/RAxML) using CASTLES-II. Here is how to do it: bin/astral4 -C -c wastral.species_tree -i your_input_gene_trees -o wastral.species_tree.with_branch_length --root your_outgroup

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26)

Hi, prof. Zhang, I inferred the weighted species tree using astral-hybrid, however, I found that sometimes few terminal branches were twice longer than the other species. Could you please tell me what causes this phenomenon? image.png (view on web) https://github.com/chaoszhang/ASTER/assets/43005382/8114a0ed-3b76-4e7a-9c86-c0af75bafd77

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XiaoTW123 commented 5 months ago

@chaoszhang Ok, i get it. Thanks for your quick reply.