binning branch length

[Grace W]

Hi everyone,

We are using RAxML v. 8.1.21 to analyze influenza data of thousands of sequence data. We have noted an issue where RAxML is binning branch lengths. I.e. the tree topology is generally accurate but there is fine-scale capping of branch lengths on a wide-spread scale. This is subtle enough not to really show up on Temp-est, but is noticeable when examining the trees carefully. This is also noted when examining the distances in the tree file. The end result is something which looks slightly like a cladogram, i.e. weird. We're using the bipartition file (with bootstraps).

Duplicates removed already but a lot of similar data

Had you encountered this before?

Looking forward to see your input.
GW

[Alexandros Stamatakis]

Dear Grace,

It could be that because the sequences are so similar you are frequently
hitting the minimum branch length value (i.e., minimum allowed length of
a branch for numerical reasons), it would be very helpful if you could
send me the tree or a screenshot (to my personal email if you prefer)
such that I can have a look to make sure I understand what you mean by
capping.

Alexis

>
> Looking forward to see your input.
> GW
>

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Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org

[Grace W]

Dear  Alexis,

Thank you so much for your reply.

I am so sorry about the long delay in response.

I consulted our group about sending the data over to you.  Unfortunately, we cannot send the raw data file to you due to restrictions of my institution and collaborators. 

I can send you a screen shot of the tree to your personal e.mail.

Looking forward to hear from you.

v/r

GW

[Alexandros Stamatakis]

You can send me the screenhsot if you like, but I can't promise that I
will be able to help you like this.

Alexis

[Grace W]

Hi Alex,

I am sending you the screen shot of the tree from my work e.mail.  Subject line will be "binning branch length".

Thanks again for your help.