Opened 10 years ago

Closed 10 years ago

Last modified 3 years ago

#633 closed defect (fixed)

moving root affects parsimony value

Reported by: westram Owned by: westram
Priority: critical Milestone: arb7.0
Component: ARB_PARSIMONY Version: SVN
Keywords: Cc:

Description (last modified by westram)

Moving the root may not have an effect on the resulting parsimony value - this is the central paradigm of the whole algorithm.

  • was first observed in [13357]
  • [13358] adds broken tests to demonstrate the bug
    • seems to happen with protein sequences only

Change History (9)

comment:1 Changed 10 years ago by westram

  • Description modified (diff)
  • Owner changed from devel to westram
  • Status changed from new to _started

comment:2 Changed 10 years ago by westram

can already be observed in current trunk:

  • load UNIT_TESTER/run/TEST_prot.arb (=same DB as used in unit test)
  • start ARB_PARS and choose REROOT MODE
  • click around and see parsimony value change

comment:3 Changed 10 years ago by westram

apparently does not happen with nucleids

  • tested with tree containing >40k species
  • tested in trunk and in branch 'pars' (both current HEAD)

comment:4 Changed 10 years ago by westram

same behavior already present in arb 5.3

comment:5 Changed 10 years ago by westram

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

by [13369]; was broken by [878]

comment:6 Changed 10 years ago by westram

This problem also caused an infinite optimization loop under certain circumstances. Strange that this was never examined by any user in the last 12 years…

comment:7 Changed 10 years ago by westram

runtime is approx. 7 times slower than before this fix :(

comment:8 Changed 9 years ago by westram

  • Milestone set to arb6.1

mark changes that got fixed after arb 6.0.x

comment:9 Changed 3 years ago by westram

  • Milestone changed from arb6.1 to arb7.0

Milestone renamed

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