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google-code-export / phyutility

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can't prune the outgroup #3

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Root tree or set of trees
2. phyutility -pr -in rooted.phy -out ingroup.phy -names T101
3.

What is the expected output? What do you see instead?
My trees consist of 100 ingroup taxa and a single outgroup taxon. I expect
to get a rooted tree consisting of only the ingroup taxa. Instead, I get
the exact same set of trees (with all taxa).

What version of the product are you using? On what operating system?
v 2.2

Please provide any additional information below.

Original issue reported on code.google.com by tra...@gmail.com on 27 Feb 2008 at 11:48

GoogleCodeExporter commented 9 years ago 
I have noticed this problem, especially if the outgroup is in a basal polytomy. 
If you would like to email me the 
file or post the file to this issue I can take a look. Otherwise, I will assume 
this is the problem and try to fix 
accordingly.

Original comment by blackrim on 28 Feb 2008 at 8:57

GoogleCodeExporter commented 9 years ago

Original comment by blackrim on 28 Feb 2008 at 8:58

GoogleCodeExporter commented 9 years ago

Original comment by blackrim on 28 Feb 2008 at 8:58

GoogleCodeExporter commented 9 years ago 
Actually the outgroup is not in a basal polytomy. I have attached all the files 
and
included a tree file of expected output (expected.phy). Here is what I did:

phyutility -rr -in unrooted.phy -out rooted.phy -names T101
phyutility -pr -in rooted.phy -out ingroup.phy -names T101

Original comment by tra...@gmail.com on 29 Feb 2008 at 6:25

Attachments:

GoogleCodeExporter commented 9 years ago 
Thanks for the files. So I can get the rooted tree. Then it has a problem 
removing the node on which the the tree 
is rooted. I have put that in the queue for fixing. Thanks for the info!

Original comment by blackrim on 29 Feb 2008 at 7:12

GoogleCodeExporter commented 9 years ago 
It has been fixed. Attached is the jar. You can just replace yours. I will 
release 2.2.1 later today and that will also 
have the fix.

Original comment by blackrim on 11 Mar 2008 at 5:39

Attachments: