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lliu1871 / phybase

Phybase provides functions to read, write, manipulate, simulate, estimate, and summarize phylogenetic trees
GNU General Public License v3.0
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How to phased all the terminal tips with a branch length equal to 1 when use Phybase simulate gene trees? #1

Open Galaxy-228 opened 2 years ago

Galaxy-228 commented 2 years ago

Hi ~ I want use Phybase to simulate gene trees (Species tree constructed by Astral), and some articles said it should phased all the terminal tips with a branch length equal to 1. Is there necessary and how to do it ? Thanks a lot !

lliu1871 commented 2 years ago
  1. The species tree must be a rooted tree with branch length.
  2. If you just want to simulate gene trees without branch lengths, the internal branch length of the species tree could be in coalescent units (time/theta) and the terminal branch length could be arbitrary (say 1).

Liang

Liang Liu Graduate Coordinator Department of Statistics Institute of Bioinformatics University of Georgia Phylogenetics Lab | Phylogenetics Lab (uga.edu)http://faculty.franklin.uga.edu/lliu/ @.***

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Hi ~ I want use Phybase to simulate gene trees (Species tree constructed by Astral), and some articles said it should phased all the terminal tips with a branch length equal to 1. Is there necessary and how to do it ? Thanks a lot !

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