Ho do I labe branches in newick ?

Chandima Ariyarathna @Chandima-Ariyarathna

05 January 2016 2 5K Report

I need to label 2 branches in a phylogenetic tree. Can somebody tell me if I have labelled the branches in these newick trees correctly. I need to use these trees in PAML to see positive selection in these branches. I have labelled the node would that be different to labelling the branches? The phylogenetic tree is attached

Thank you very much

chandima

Branch 2

(OsHKT11:0.587799,OsHKT13:0.3677219999999999,((OsHKT15:0.502488,TmHKT141:0.695629):0.25236000000000014,((OsHKt21:0.17423499999999992,(L823634:0.10184700000000002,((21acDNA:0.02246400000000004,21d:0.023975999999999997):0.01638699999999993,(21BcDNA:0.02215900000000004,AM00005:0.0511569999999999):0.013416000000000095):0.050529999999999964):0.07750600000000007):0.24453400000000003,((Sb251700:0.07577699999999998,ZM2G1356:0.1177109999999999):0.37270800000000004,((OsHKT23:0.02419299999999991,OsHKT24:0.021389000000000102):0.16342100000000004,((Bra34210:0.0,L100846:0.0):0.08045600000000008,(22BcDNA:0.02155499999999999,((22AcDNA:0.01854099999999992,22DcDNA:0.009038000000000102):0.01695599999999997,AK37002:0.03680799999999995):0.005055999999999949):0.06552399999999992):0.03808900000000004):0.099661)#1:0.17251799999999995):0.3580960000000002):0.3620859999999999);

Branch 1

(OsHKT11:0.587799,OsHKT13:0.3677219999999999,((OsHKT15:0.502488,TmHKT141:0.695629):0.25236000000000014,((OsHKt21:0.17423499999999992,(L823634:0.10184700000000002,((21acDNA:0.02246400000000004,21d:0.023975999999999997):0.01638699999999993,(21BcDNA:0.02215900000000004,AM00005:0.0511569999999999):0.013416000000000095):0.050529999999999964):0.07750600000000007) #1:0.24453400000000003,((Sb251700:0.07577699999999998,ZM2G1356:0.1177109999999999):0.37270800000000004,((OsHKT23:0.02419299999999991,OsHKT24:0.021389000000000102):0.16342100000000004,((Bra34210:0.0,L100846:0.0):0.08045600000000008,(22BcDNA:0.02155499999999999,((22AcDNA:0.01854099999999992,22DcDNA:0.009038000000000102):0.01695599999999997,AK37002:0.03680799999999995):0.005055999999999949):0.06552399999999992):0.03808900000000004):0.099661):0.17251799999999995):0.3580960000000002):0.3620859999999999);

Tyler Chafin

See page 15 of the PAML manual, under the subsection "Tree file format and representations of tree topology". What you have looks correct to me. The manual suggests checking your labeling by loading your tree into TreeView.

http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf

Patrice Showers Corneli

You could also load it into Fig Tree (Rambout).

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