nwkit shuffle

Overview

nwkit shuffle shuffles branches and/or labels.

Examples

Command

nwkit shuffle --infile input.nwk --outfile output.nwk --label yes --branch_length no --topology yes

input.nwk

(((((Cephalotus_follicularis_Cfol-v3-04540:0.164307,(Populus_trichocarpa_Potri.008G189000.1:0.09287,Populus_trichocarpa_Potri.010G042400.3:0.052659)n75:0.121871)n78:1e-06,Arabidopsis_thaliana_AT1G23420.1:0.256958)n81:0.175591,Oryza_sativa_LOC-Os07g38410.1:0.50575)n84:0.346043,((Arabidopsis_thaliana_AT2G26580.1:0.101605,((Cephalotus_follicularis_Cfol-v3-04239:0.229394,Cephalotus_follicularis_Cfol-v3-25951:0.057497)n90:0.023987,(Populus_trichocarpa_Potri.006G067800.1:0.022676,Populus_trichocarpa_Potri.018G129800.1:0.036573)n93:0.03899)n96:0.037252)n99:0.151886,(((Cephalotus_follicularis_Cfol-v3-07401:0.123537,Populus_trichocarpa_Potri.016G067300.2:0.266657)n105:0.129157,(Oryza_sativa_LOC-Os03g44710.2:0.143862,Oryza_sativa_LOC-Os12g42610.1:0.189098)n108:0.169404)n111:0.083281,(Oryza_sativa_LOC-Os07g06620.2:0.595599,((Populus_trichocarpa_Potri.001G214700.2:0.11244,Populus_trichocarpa_Potri.009G000100.1:0.237723)n117:0.200465,Arabidopsis_thaliana_AT1G08465.1:0.237149)n120:0.013353)n123:0.021313)n115:0.100647)n103:0.098343)n88:0.050338,((((Oryza_sativa_LOC-Os02g42950.1:0.108866,Oryza_sativa_LOC-Os04g45330.1:0.115914)n33:0.096243,Oryza_sativa_LOC-Os10g36420.1:0.264804)n36:0.161537,(((Cephalotus_follicularis_Cfol-v3-15267:0.083041,(Populus_trichocarpa_Potri.002G145100.1:0.051013,Populus_trichocarpa_Potri.014G066700.1:0.048684)n39:0.03858)n42:0.058161,(Cephalotus_follicularis_Cfol-v3-19081:0.066738,(Populus_trichocarpa_Potri.001G120200.1:0.057203,Populus_trichocarpa_Potri.003G112800.1:0.021102)n45:0.038314)n48:0.090719)n51:0.045401,(Arabidopsis_thaliana_AT2G45190.1:0.15491,Arabidopsis_thaliana_AT4G00180.1:0.256491)n54:0.050042)n57:0.092595)n60:0.030363,(((Cephalotus_follicularis_Cfol-v3-28822:0.063825,Populus_trichocarpa_Potri.008G097800.1:0.226581)n63:0.078393,Arabidopsis_thaliana_AT1G69180.1:0.265871)n66:0.067694,Oryza_sativa_LOC-Os03g11600.1:0.330355)n69:0.496564)n72:0.050338)n214:0;

output.nwk (trial 1)

((((Cephalotus_follicularis_Cfol-v3-04239:0.266657,(Populus_trichocarpa_Potri.001G120200.1:0.164307,Populus_trichocarpa_Potri.009G000100.1:0.266657):0.057497):0.123537,(Populus_trichocarpa_Potri.010G042400.3:0.057497,Arabidopsis_thaliana_AT2G45190.1:0.256491):0.048684):0.237149,((Cephalotus_follicularis_Cfol-v3-28822:0.50575,(Cephalotus_follicularis_Cfol-v3-19081:0.330355,Populus_trichocarpa_Potri.008G097800.1:0.237149):0.115914):0.052659,(Cephalotus_follicularis_Cfol-v3-25951:0.265871,Populus_trichocarpa_Potri.018G129800.1:0.15491):0.052659):0.108866):0.11244,((((Populus_trichocarpa_Potri.003G112800.1:0.50575,Cephalotus_follicularis_Cfol-v3-04540:0.229394):0.265871,(Oryza_sativa_LOC-Os03g44710.2:0.15491,Populus_trichocarpa_Potri.006G067800.1:0.051013):0.101605):0.237723,(((Arabidopsis_thaliana_AT2G26580.1:0.264804,(Arabidopsis_thaliana_AT1G08465.1:0.330355,Cephalotus_follicularis_Cfol-v3-07401:0.09287):0.083041):0.09287,Populus_trichocarpa_Potri.016G067300.2:0.066738):0.226581,((Oryza_sativa_LOC-Os02g42950.1:0.595599,(Populus_trichocarpa_Potri.001G214700.2:0.083041,(Cephalotus_follicularis_Cfol-v3-15267:0.256491,Arabidopsis_thaliana_AT1G23420.1:0.123537):0.143862):0.101605):0.051013,((Oryza_sativa_LOC-Os03g11600.1:0.189098,(Populus_trichocarpa_Potri.014G066700.1:0.164307,Oryza_sativa_LOC-Os10g36420.1:0.022676):0.143862):0.063825,(Arabidopsis_thaliana_AT4G00180.1:0.063825,(Populus_trichocarpa_Potri.002G145100.1:0.264804,(Arabidopsis_thaliana_AT1G69180.1:0.048684,Oryza_sativa_LOC-Os12g42610.1:0.11244):0.057203):0.022676):0.036573):0.237723):0.595599):0.021102):0.229394,((Oryza_sativa_LOC-Os07g38410.1:0.256958,Populus_trichocarpa_Potri.008G189000.1:0.057203):0.115914,(Oryza_sativa_LOC-Os07g06620.2:0.036573,Oryza_sativa_LOC-Os04g45330.1:0.108866):0.256958):0.189098):0.021102):0;

output.nwk (trial 2)

((((Populus_trichocarpa_Potri.002G145100.1:0.189098,(Cephalotus_follicularis_Cfol-v3-15267:0.115914,(Arabidopsis_thaliana_AT1G69180.1:0.066738,Cephalotus_follicularis_Cfol-v3-07401:0.15491):0.264804):0.048684):0.063825,(Populus_trichocarpa_Potri.006G067800.1:0.022676,(Cephalotus_follicularis_Cfol-v3-04239:0.052659,(Arabidopsis_thaliana_AT1G23420.1:0.226581,Populus_trichocarpa_Potri.001G120200.1:0.11244):0.256958):0.057497):0.101605):0.595599,(((Oryza_sativa_LOC-Os03g44710.2:0.108866,(Cephalotus_follicularis_Cfol-v3-04540:0.237723,Arabidopsis_thaliana_AT2G26580.1:0.108866):0.595599):0.143862,((Oryza_sativa_LOC-Os07g38410.1:0.237149,(Cephalotus_follicularis_Cfol-v3-19081:0.057203,Populus_trichocarpa_Potri.008G189000.1:0.256491):0.101605):0.051013,((Populus_trichocarpa_Potri.014G066700.1:0.237723,(Oryza_sativa_LOC-Os04g45330.1:0.15491,Populus_trichocarpa_Potri.001G214700.2:0.266657):0.048684):0.330355,(Populus_trichocarpa_Potri.016G067300.2:0.123537,Cephalotus_follicularis_Cfol-v3-25951:0.164307):0.256958):0.265871):0.189098):0.164307,((Oryza_sativa_LOC-Os12g42610.1:0.063825,Populus_trichocarpa_Potri.008G097800.1:0.50575):0.052659,(Populus_trichocarpa_Potri.010G042400.3:0.066738,Oryza_sativa_LOC-Os03g11600.1:0.115914):0.266657):0.021102):0.264804):0.330355,((Arabidopsis_thaliana_AT2G45190.1:0.057497,(Arabidopsis_thaliana_AT4G00180.1:0.036573,Cephalotus_follicularis_Cfol-v3-28822:0.229394):0.256491):0.11244,((Oryza_sativa_LOC-Os10g36420.1:0.051013,(Populus_trichocarpa_Potri.009G000100.1:0.123537,(Arabidopsis_thaliana_AT1G08465.1:0.021102,(Oryza_sativa_LOC-Os07g06620.2:0.237149,Oryza_sativa_LOC-Os02g42950.1:0.143862):0.09287):0.083041):0.265871):0.057203,(Populus_trichocarpa_Potri.018G129800.1:0.50575,Populus_trichocarpa_Potri.003G112800.1:0.022676):0.229394):0.226581):0.09287):0;

output.nwk (trial 3)

(((Cephalotus_follicularis_Cfol-v3-04239:0.108866,(Cephalotus_follicularis_Cfol-v3-15267:0.101605,Cephalotus_follicularis_Cfol-v3-19081:0.021102):0.09287):0.264804,((Populus_trichocarpa_Potri.001G120200.1:0.063825,(Populus_trichocarpa_Potri.009G000100.1:0.143862,Populus_trichocarpa_Potri.014G066700.1:0.066738):0.256491):0.264804,((Populus_trichocarpa_Potri.002G145100.1:0.15491,(Populus_trichocarpa_Potri.001G214700.2:0.115914,(Oryza_sativa_LOC-Os07g38410.1:0.115914,(Arabidopsis_thaliana_AT1G69180.1:0.021102,Arabidopsis_thaliana_AT2G26580.1:0.052659):0.266657):0.237149):0.11244):0.595599,((Arabidopsis_thaliana_AT1G08465.1:0.237723,Populus_trichocarpa_Potri.003G112800.1:0.048684):0.051013,(Populus_trichocarpa_Potri.008G097800.1:0.123537,Cephalotus_follicularis_Cfol-v3-07401:0.048684):0.108866):0.057203):0.15491):0.330355):0.50575,((Populus_trichocarpa_Potri.016G067300.2:0.237149,(Cephalotus_follicularis_Cfol-v3-28822:0.057203,Oryza_sativa_LOC-Os07g06620.2:0.083041):0.189098):0.066738,((Oryza_sativa_LOC-Os10g36420.1:0.143862,Populus_trichocarpa_Potri.018G129800.1:0.051013):0.189098,((Populus_trichocarpa_Potri.010G042400.3:0.265871,Oryza_sativa_LOC-Os03g44710.2:0.595599):0.022676,((Arabidopsis_thaliana_AT1G23420.1:0.229394,(Populus_trichocarpa_Potri.008G189000.1:0.266657,(Oryza_sativa_LOC-Os03g11600.1:0.022676,(Cephalotus_follicularis_Cfol-v3-25951:0.123537,Cephalotus_follicularis_Cfol-v3-04540:0.226581):0.036573):0.229394):0.063825):0.09287,(Arabidopsis_thaliana_AT4G00180.1:0.330355,(Oryza_sativa_LOC-Os02g42950.1:0.101605,(Populus_trichocarpa_Potri.006G067800.1:0.50575,(Arabidopsis_thaliana_AT2G45190.1:0.265871,(Oryza_sativa_LOC-Os12g42610.1:0.256958,Oryza_sativa_LOC-Os04g45330.1:0.057497):0.11244):0.164307):0.036573):0.256491):0.164307):0.226581):0.057497):0.052659):0.237723):0;