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rrnewton / PhyBin

Binning (Newick) Phylogenetic Trees by Topology
http://people.csail.mit.edu/newton/phybin
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Internal invariant broken: equally good roots #12

Open rrnewton opened 7 years ago

rrnewton commented 7 years ago

(Reported by Stefanie Hartmann)

This has to do with an internal algorithm that Phybin uses to pick "canonical" roots so that comparing unrooted trees becomes as easy as comparing rooted trees.

Clearly the algorithm has failed in this case:

../software/phybin-0.3.x86_64_linux --bin alnsTrees -o testPhybin
Input is a directory, reading all regular files contained (4954 regular files found):  "alnsTrees"
Cleaning away previous phybin outputs...
Parsing 4954 Newick tree files.

Total unique taxa (5):
  out tx2 tx1 tx4 tx3
Note: defaulting to expecting ALL 5 to be present..

Number of input tree files: 4954
Number of VALID trees (correct # of leaves/taxa): 4954
Total tree nodes contained in valid trees: 24770
Average branch len over valid trees: 4.202208347174017e-4
Max/Min branch lengths: (1.4016067376624779e-3,0.0)
Creating equivalence classes (bins)...
phybin-0.3.x86_64_linux: 
Internal invariant broken.  These two were equally good roots:
NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 4.65012928950792e-4 Nothing) 0,
                                        NTInterior (StandardDecor 4.65012928950792e-4 Nothing) [NTInterior (StandardDecor 2.746891336353709e-4 Nothing) [NTLeaf (StandardDecor 6.458761735702267e-4 Nothing) 1,
                                                                                                                                                         NTLeaf (StandardDecor 3.7263852482769005e-4 Nothing) 2],
                                                                                                NTInterior (StandardDecor 2.3283439723368005e-4 Nothing) [NTLeaf (StandardDecor 6.696724461805924e-4 Nothing) 3,
                                                                                                                                                          NTLeaf (StandardDecor 5.391785869970742e-4 Nothing) 4]]]
NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 4.65012928950792e-4 Nothing) 0,
                                        NTInterior (StandardDecor 0.0 Nothing) [NTInterior (StandardDecor 4.65012928950792e-4 Nothing) [NTInterior (StandardDecor 2.746891336353709e-4 Nothing) [NTLeaf (StandardDecor 6.458761735702267e-4 Nothing) 1,
                                                                                                                                                                                                 NTLeaf (StandardDecor 3.7263852482769005e-4 Nothing) 2],
                                                                                                                                        NTInterior (StandardDecor 2.3283439723368005e-4 Nothing) [NTLeaf (StandardDecor 6.696724461805924e-4 Nothing) 3,
                                                                                                                                                                                                  NTLeaf (StandardDecor 5.391785869970742e-4 Nothing) 4]]]]
harris-2374 commented 3 years ago

I have been running into this same issue and I was wondering if there have been any updates to resolve this? Thanks!

` Cleaning away previous phybin outputs... Parsing 24200 Newick tree files.

Total unique taxa (5): tx1 tx2 tx3 tx4 tx5 Note: defaulting to expecting ALL 5 to be present..

Number of input tree files: 24200 Number of VALID trees (correct # of leaves/taxa): 24200 Total tree nodes contained in valid trees: 121000 Average branch len over valid trees: 0.0 Max/Min branch lengths: (0.0,0.0) Creating equivalence classes (bins)... phybin: Internal invariant broken. These two were equally good roots: NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 4, NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 3, NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 2, NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 0, NTLeaf (StandardDecor 0.0 Nothing) 1]]]] NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 4, NTInterior (StandardDecor 0.0 Nothing) [NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 3, NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 2, NTInterior (StandardDecor 0.0 Nothing) [NTLeaf (StandardDecor 0.0 Nothing) 0, NTLeaf (StandardDecor 0.0 Nothing) 1]]]]] `