[bug] Newick files in 3.5.1 have branch lengths of 0.0 #202
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Fixed in 3.5.3 |
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The conversion to presence/absence of accessory genes to Newick files goes wrong since the update to 3.5.1. The .fa file contains only C's, and hence there is no difference visible.
This is tested with datasets that previously gave clear differences.
Summary file:
Core genes (99% <= strains <= 100%): 1461
Soft core genes (95% <= strains < 99%): 765
Shell genes (15% <= strains < 95%): 1389
Cloud genes (0% <= strains < 15%): 7657
Total genes: 11272
So branch lengths of 0 are not expected.
The Newick file looks like this:
(L1_Lm_10KSM:0.0,L1_Lm_11KSM:0.0,L1_Lm_13KSM:0.0,L1_Lm_15KSM:0.0,L1_Lm_4KSM:0.0,L1_Lm_6KSM:0.0,L1_Lm_8KSM:0.0,L1_Lm_BHU1:0.0,L1_Lm_BHU2:0.0,L1_Lm_BHU3:0.0, etc
The .fa file says:
(etc)
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