Opened 15 years ago

Closed 15 years ago

#157 closed defect (fixed)

DNAPARS removes sequences from tree and produces zombies

Reported by: fog Owned by: westram
Priority: blocker Milestone:
Component: ARB_NTREE Version: SVN
Keywords: Cc:

Description

DNAPARS removes at least 2 sequences from the tree and produces 1 zombie. This seems to be a problem with all Phylip programs. Seems to be a problem when the sequences are mapped back to ARB - 11 sequences are send to DNApars but only 8 come back.

Attachments (1)

treeimport​ (661 bytes) - added by epruesse 15 years ago.

Download all attachments as: .zip

Change History (8)

comment:1 Changed 15 years ago by fog

Further checks of the outtree file showed, that the new ARB has problems with importing treefiles that are not written in a single line. Example: 

((PrhVib23:0.02171,(((PrhVib24:0.02754,PrhAes15:0.01433):0.02636,
I56Thala:0.10115):0.01540,((H17Lute2:0.01045,CluPhae5:0.01102):0.00672,
(CluLim20:0.01127,(CluPha17:0.01388,H17Phaeo:0.02244):0.01051):0.00948):0.01139):0.01137):0.01391,
CblThio5:0.02299,CblTepi2:0.01794);

does not work (two species are not imported and one Zombie is produced
while (everything in one line) 

((PrhVib23:0.02171,((PrhVib24:0.02754,PrhAes15:0.01433):0.02636,I56Thala:0.10115):0.01540,((H17Lute2:0.01045,CluPhae5:0.01102):0.00672,(CluLim20:0.01127,(CluPha17
:0.01388,H17Phaeo:0.02244):0.01051):0.00948):0.01139):0.01137):0.01391,CblThio5:0.02299,CblTepi2:0.01794);

works fine.

comment:2 Changed 15 years ago by westram

  • Owner changed from devel to westram
  • Status changed from new to assigned

comment:3 Changed 15 years ago by epruesse

  • Resolution set to fixed
  • Status changed from assigned to closed

Unable to reproduce bug with r5931 — seems to be fixed.

comment:4 Changed 15 years ago by fog

  • Resolution fixed deleted
  • Status changed from closed to reopened

Unfortunately I have to disagree. Took LTP95 e.g. /megx/home/fog/arb/testdb/LTPs95_opt_fog_cut_test.arb 10 sequences are marked - made tree with DNAPars, Phylip Distance Methods and got between 9-10 sequences in the tree.

Sorry

comment:5 Changed 15 years ago by fog

11 sequences were marked…

Changed 15 years ago by epruesse

comment:6 Changed 15 years ago by epruesse

attached patch fixed the issue

comment:7 Changed 15 years ago by westram

  • Resolution set to fixed
  • Status changed from reopened to closed
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