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I'm wondering whether we could provide an example NHX file that has duplication on the repo.
This is an example NHX file with duplication events but it doesn't have species information
((((Q8SXG7,D6WTQ2)Holometabola,(B7PEN0,B7P8T8)[&&NHX:Ev=duplication])Arthropoda,(((((Q4KM14,A0A8M1N7C7)[&&NHX:Ev=duplication],H2MDH4)Clupeocephala,W5N6H4)Neopterygii,A0A1D5NX87)Euteleostomi,(C3Y1C3,(((Q503H1,H2M3Q7)Clupeocephala,W5M8W6)Neopterygii,((E1BZH5,((((G3QLT4,Q9NX07,H2PYH3)Homininae,(Q80VC6,Q9QZI7)Murinae)Euarchontoglires,(Q1RMJ7,A0A8I3ND40)Laurasiatheria)Boreoeutheria,A0A5F8HF32)Theria)Amniota,(Q0VFK2,A0A8J1JT11)[&&NHX:Ev=duplication])Tetrapoda)Euteleostomi)Chordata)[&&NHX:Ev=duplication])Bilateria,A7SW98)Eumetazoa;
This has species info but no duplication events.
((A_s1:0.1[&&NHX:conf=0.9:S=s1],B_s2:0.2[&&NHX:conf=0.8:S=s2])[&&NHX:S=speciesA],C_s3:0.3[&&NHX:S=speciesB]);
About this example, it doesn't need to have species info both in NHX format and in the leaf name, right?
And about another example
((HUMAN_A, HUMAN_B)[&&NHX:E=S], MOUSE_B)[&&NHX:E=S];
Shouldn't E be a duplication node?
Thanks!
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