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update after re-build

The purpose of this rebuild was to fix an error that used to occur in TreeTime, that made some branches with minimal genetic changes be much too long in the temporally resolved version of the tree. The new tree uses the new treetime code whereby temporally resolved branch lengths do sync with genetic distance branch lengths.
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alliblk committed Feb 9, 2019
1 parent 19e6aa3 commit cfb01f931acef88d87d387407851d221468c6391
Showing with 41,903 additions and 50,265 deletions.
  1. +297 −297 auspice/zika-colombia_meta.json
  2. +21,857 −29,844 auspice/zika-colombia_tree.json
  3. +4,557 −4,690 results/aa_muts.json
  4. +9 −9 results/aligned.fasta.log
  5. +6,218 −6,317 results/branch_lengths.json
  6. +76 −76 results/country.mugration_model.txt
  7. +4,103 −4,136 results/nt_muts.json
  8. +10 −10 results/region.mugration_model.txt
  9. +4,774 −4,884 results/traits.json
  10. +1 −1 results/tree.nwk
  11. +1 −1 results/tree_raw.nwk

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@@ -5,21 +5,21 @@ C: south_america
D: ?


Substitution rate (mu): 25.387006
Substitution rate (mu): 21.985781

Equilibrium frequencies (pi_i):
A: 0.3194
B: 0.2812
C: 0.3993
A: 0.5635
B: 0.2631
C: 0.1734

Symmetrized rates from j->i (W_ij):
A B C
A 0 0.8816 2.4415
B 0.8816 0 0.9738
C 2.4415 0.9738 0
A 0 0.4135 4.1931
B 0.4135 0 0.6368
C 4.1931 0.6368 0

Actual rates from j->i (Q_ij):
A B C
A 0 0.2816 0.7799
B 0.2479 0 0.2739
C 0.975 0.3888 0
A 0 0.233 2.3628
B 0.1088 0 0.1676
C 0.727 0.1104 0
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