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ContentMine / phylotree

A repository for ami-phylotree development
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Multiple branches in output #18

Open petermr opened 9 years ago

petermr commented 9 years ago

in ijs_0_000364_0_003 the output appears to have a trifurcation. What does this do to downstream programs. Do they:

Here's the Newick

(((((:195.0,:135.0)NT1.25:86.0,:301.0)NT1.17:131.0,(:251.0,:364.0)NT1.15:106.0)NT1.5:12.0,(:223.0,:333.0)NT1.19:158.0)NT1.2:10.0,((:441.0,(((:295.0,((((:140.0,:164.0)NT1.28:63.0,:165.0)NT1.22:24.0,(:183.0,:185.0)NT1.26:55.0)NT1.21:78.0,(:186.0,:194.0)NT1.23:105.0)NT1.14:56.0)NT1.10:21.0,(:279.0,:302.0)NT1.16:107.0)NT1.8:8.0,((:189.0,:191.0)NT1.27:187.0,:343.0)NT1.12:55.0)NT1.6:11.0,:497.0)NT1.3:6.0,((:348.0,(:124.0,:167.0)NT1.24:205.0)NT1.7:12.0,(:484.0,((:260.0,:320.0)NT1.13:33.0,((:157.0,:181.0)NT1.20:21.0,:152.0)NT1.18:91.0)NT1.11:22.0)NT1.9:32.0)NT1.4:11.0)NT1.1:9.0)NT1.60;

(Tip labels have been lost - can be restored if necessary)

IOW does ami-phylo have to break multifurcations into binary?

rossmounce commented 9 years ago

Most programs should be fine with this. I'm on a mobile atm but will properly test that exact newick string later tonight. I expect it'll be okay.

Absolutely do not 'break' multifurcations into binary. If the original image implies a multifurcation (polytomy) then we should preserve that information. Very bad to arbitrarily break polytomies, best avoided if at all possible.

rossmounce commented 9 years ago

Managed to do it entirely on my phone. Tested at http://www.unc.edu/~bdmorris/treelib-js/demo.html had to add tip labels.

rossmounce commented 9 years ago

(((((A:195.0,b:135.0)NT1.25:86.0,c:301.0)NT1.17:131.0,(d:251.0,e:364.0)NT1.15:106.0)NT1.5:12.0,(f:223.0,g:333.0)NT1.19:158.0)NT1.2:10.0,((h:441.0,(((i:295.0,((((j:140.0,k:164.0)NT1.28:63.0,l:165.0)NT1.22:24.0,(m:183.0,n:185.0)NT1.26:55.0)NT1.21:78.0,(o:186.0,p:194.0)NT1.23:105.0)NT1.14:56.0)NT1.10:21.0,(q:279.0,r:302.0)NT1.16:107.0)NT1.8:8.0,((s:189.0,t:191.0)NT1.27:187.0,u:343.0)NT1.12:55.0)NT1.6:11.0,v:497.0)NT1.3:6.0,((w:348.0,(x:124.0,y:167.0)NT1.24:205.0)NT1.7:12.0,(z:484.0,((aa:260.0,bb:320.0)NT1.13:33.0,((cc:157.0,dd:181.0)NT1.20:21.0,ee:152.0)NT1.18:91.0)NT1.11:22.0)NT1.9:32.0)NT1.4:11.0)NT1.1:9.0)NT1.60;

rossmounce commented 9 years ago

Screenshot of visualized Newick string here:

screenshot