Astral v.5.6.2 the resulting species tree has some branch lengths are negative

[ghost]

I use 91 gene tree to produce a species tree, and with this one, I would compare the difference between contenation and coalascence.
when I imported this species tree into R, wanting to transfer it to ultrametric format, but there are some output error for this tree. there it is:

I checked this tree, no found any negative value. How to explain this? Is it a bug for Astral?

[smirarab]

ASTRAL currently does not output branch lengths for terminal branches. That is probably the root of the issue. If you want an ultrametric tree only for visualization purposes, just add a constant branch length to all terminals. Use your favorite approach to do that. If you found no alternatives, check out this script: https://github.com/smirarab/global/blob/master/src/mirphyl/utils/add-bl.py If you want an ultrametric tree for dating, I don't think there is currently any good way of doing that using ASTRAL branch lengths.

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On Mon, Sep 10, 2018 at 5:40 PM MeiyuanJi ***@***.***> wrote: I use 91 gene tree to produce a species tree, and with this one, I would compare the difference between contenation and coalascence. when I imported this species tree into R, wanting to transfer it to ultrametric format, but there are some output error for this tree. there it is: [image: default] <https://user-images.githubusercontent.com/33933620/45331590-31d06000-b59e-11e8-8b9c-bcd0ee8c3a0b.png> I checked this tree, no found any negative value. How to explain this? Is it a bug for Astral? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#37>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAybuCeeI7ALw3DvmdmaKCt0NUTPfxaFks5uZwaZgaJpZM4WiZw8> .

-- Siavash Mirarab