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nwkit nhx2nwk
Kenji Fukushima edited this page Mar 9, 2023
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nwkit nhx2nwk converts NHX format into Newick format. See here for details on the formats.
nwkit nhx2nwk --infile input.nhx --outfile output.nwk --node_label "S"
((((Arabidopsis_thaliana_AT2G26580.1:0.028662[&&NHX:S=Arabidopsis_thaliana:D=N:H=N:B=0.028662],Capsella_rubella_Carub.0004s0684.1:0.068238[&&NHX:S=Capsella_rubella:D=N:H=N:B=0.068238])n54:0.374004[&&NHX:S=s2:D=N:H=N:B=0.374004],((Arabidopsis_thaliana_AT1G08465.1:0.047957[&&NHX:S=Arabidopsis_thaliana:D=N:H=N:B=0.047957],Capsella_rubella_Carub.0001s0782.1:0.058352[&&NHX:S=Capsella_rubella:D=N:H=N:B=0.058352])n60:0.399242[&&NHX:S=s2:D=N:H=N:B=0.399242],Utricularia_gibba_unitig_26.g9420.t1:0.418901[&&NHX:S=Utricularia_gibba:D=N:H=N:B=0.418901])n63:0.144393[&&NHX:S=s1:D=N:H=N:B=0.144393])n58:0.248198[&&NHX:S=s1:D=Y:H=N:B=0.248198],(((Arabidopsis_thaliana_AT4G00180.1:0.025227[&&NHX:S=Arabidopsis_thaliana:D=N:H=N:B=0.025227],Capsella_rubella_Carub.0006s3704.1:0.064539[&&NHX:S=Capsella_rubella:D=N:H=N:B=0.064539])n18:0.23903[&&NHX:S=s2:D=N:H=N:B=0.23903],((Utricularia_gibba_unitig_0.g2762.t1:0.959728[&&NHX:S=Utricularia_gibba:D=N:H=N:B=0.959728],Utricularia_gibba_unitig_8.g3329.t1:0.105402[&&NHX:S=Utricularia_gibba:D=N:H=N:B=0.105402])n21:0.111763[&&NHX:S=Utricularia_gibba:D=Y:H=N:B=0.111763],((Utricularia_gibba_unitig_26.g8895.t1:0.23784[&&NHX:S=Utricularia_gibba:D=N:H=N:B=0.23784],Utricularia_gibba_unitig_76.g29081.t1:0.12065[&&NHX:S=Utricularia_gibba:D=N:H=N:B=0.12065])n24:0.262545[&&NHX:S=Utricularia_gibba:D=Y:H=N:B=0.262545],Utricularia_gibba_unitig_749.g13777.t1:0.262936[&&NHX:S=Utricularia_gibba:D=N:H=N:B=0.262936])n27:0.102423[&&NHX:S=Utricularia_gibba:D=Y:H=N:B=0.102423])n30:0.144539[&&NHX:S=Utricularia_gibba:D=Y:H=N:B=0.144539])n33:0.071478[&&NHX:S=s1:D=N:H=N:B=0.071478],(Capsella_rubella_Carub.0004s2781.1:0.022543[&&NHX:S=Capsella_rubella:D=N:H=N:B=0.022543],Arabidopsis_thaliana_AT2G45190.1:0.029052[&&NHX:S=Arabidopsis_thaliana:D=N:H=N:B=0.029052])n36:0.174701[&&NHX:S=s2:D=N:H=N:B=0.174701])n39:0.273494[&&NHX:S=s1:D=Y:H=N:B=0.273494])n53:1e-06[&&NHX:S=s1:D=Y:H=N:B=1e-06],((Arabidopsis_thaliana_AT1G23420.1:0.002487[&&NHX:S=Arabidopsis_thaliana:D=N:H=N:B=0.002487],Capsella_rubella_Carub.0001s2300.1:0.064109[&&NHX:S=Capsella_rubella:D=N:H=N:B=0.064109])n42:1.08579[&&NHX:S=s2:D=N:H=N:B=1.08579],(Arabidopsis_thaliana_AT1G69180.1:0.041529[&&NHX:S=Arabidopsis_thaliana:D=N:H=N:B=0.041529],Capsella_rubella_Carub.0002s1578.1:0.036012[&&NHX:S=Capsella_rubella:D=N:H=N:B=0.036012])n45:1.17872[&&NHX:S=s2:D=N:H=N:B=1.17872])n48:1e-06[&&NHX:S=s2:D=Y:H=N:B=1e-06])n119[&&NHX:S=s1:D=Y:H=N:B=0];
((((Arabidopsis_thaliana_AT2G26580.1:0.028662,Capsella_rubella_Carub.0004s0684.1:0.068238)s2:0.374004,((Arabidopsis_thaliana_AT1G08465.1:0.047957,Capsella_rubella_Carub.0001s0782.1:0.058352)s2:0.399242,Utricularia_gibba_unitig_26.g9420.t1:0.418901)s1:0.144393)s1:0.248198,(((Arabidopsis_thaliana_AT4G00180.1:0.025227,Capsella_rubella_Carub.0006s3704.1:0.064539)s2:0.23903,((Utricularia_gibba_unitig_0.g2762.t1:0.959728,Utricularia_gibba_unitig_8.g3329.t1:0.105402)Utricularia_gibba:0.111763,((Utricularia_gibba_unitig_26.g8895.t1:0.23784,Utricularia_gibba_unitig_76.g29081.t1:0.12065)Utricularia_gibba:0.262545,Utricularia_gibba_unitig_749.g13777.t1:0.262936)Utricularia_gibba:0.102423)Utricularia_gibba:0.144539)s1:0.071478,(Capsella_rubella_Carub.0004s2781.1:0.022543,Arabidopsis_thaliana_AT2G45190.1:0.029052)s2:0.174701)s1:0.273494)s1:1e-06,((Arabidopsis_thaliana_AT1G23420.1:0.002487,Capsella_rubella_Carub.0001s2300.1:0.064109)s2:1.08579,(Arabidopsis_thaliana_AT1G69180.1:0.041529,Capsella_rubella_Carub.0002s1578.1:0.036012)s2:1.17872)s2:1e-06)s1:0;