Hi,
I want to construct a phylogenetic tree with ape package. I have a csv file
with gene ids and copy number for each gene across different samples. I want to
construct phylogenetic tree. I am wondering how could I convert the csv file to
input file for ape. Could you please suggest me how can I convert csv file to
input file that is acceptable by ape?
Thanks
Ranjita
GENE,SAMN05064989,SAMN05064990,SAMN05064991,SAMN05064992,SAMN05064993,SAMN05064994,SAMN05064995,SAMN05064996,SAMN05064997,SAMN05064998,SAMN05064999,SAMN05065000,SAMN05065001
MD00G1000200,1.999678,2.644484,1.843331,1.868703,2.034242,1.752502,1.859093,2.039209,2.441564,2.711497,2.184576,1.473055,1.876445
MD00G1000300,1.415342,1.48209,1.549128,1.706571,2.046146,1.158263,1.646863,1.173129,1.59711,1.738894,1.419168,1.371778,1.568272
MD00G1000400,1.398499,1.797129,1.802143,1.166775,1.390045,1.236685,1.314259,1.58712,1.303329,1.782833,1.305629,1.461014,1.712468
MD00G1000500,2.41541,4.003027,2.883078,2.829228,2.876289,2.686079,2.253276,2.52543,2.45406,3.053208,3.668503,3.119604,2.609322
MD00G1000600,1.357889,1.514805,1.754632,1.905162,1.853981,1.248514,1.889641,1.832417,1.537696,1.39775,1.808635,1.389049,1.623491
MD00G1000700,1.629476,2.228273,2.048752,1.74234,1.974563,1.961737,2.069386,1.617159,1.82523,1.496132,2.092336,2.065827,1.946314
MD00G1000800,1.896418,2.22733,1.985247,1.983065,1.83869,1.9923,1.68222,1.750361,1.779146,2.209676,1.973086,1.981803,1.630689
MD00G1000900,3.134369,2.734057,2.550392,3.401735,3.493074,2.421759,2.86019,3.21655,2.768818,2.675039,3.344572,2.324965,2.332387
MD00G1001000,1.933826,1.876517,2.021223,1.739334,1.900607,1.864082,1.791559,1.847408,1.798716,2.155571,1.955044,2.377852,1.829788
MD00G1001100,0.945261,1.069836,1.105532,1.39809,1.147328,1.434332,1.195645,0.999553,0.836034,1.329002,1.742932,0.969243,1.431592
MD00G1001200,2.231896,2.332669,3.101326,2.176223,3.526095,2.718395,2.382203,2.327535,2.215922,1.528227,2.62628,2.409097,3.385232
MD00G1001300,4.502762,3.921681,4.116981,3.10278,3.640254,3.509639,3.559179,3.580477,3.159958,3.558723,4.421366,4.787455,4.684205
MD00G1001400,2.236153,2.537318,2.032665,2.0862,2.509157,2.348267,2.240651,2.156838,1.998623,2.466158,2.506128,2.508376,2.115701
MD00G1001500,2.238276,2.20046,2.405819,2.438955,2.578238,2.362307,2.68222,2.044836,2.145149,2.553174,2.299561,2.901258,2.219329
MD00G1001700,12.567245,11.491921,12.917022,9.731756,10.496296,10.999282,10.04299,11.116823,11.920293,10.890662,10.974454,9.573012,10.618516
MD00G1001800,2.255836,2.143793,2.275005,2.017084,2.705015,2.045186,2.490839,2.174137,2.108093,2.173543,2.182403,1.969187,2.330892
MD00G1001900,2.611557,3.243386,2.359358,2.605919,2.039701,2.751724,2.535086,2.946174,2.491261,2.874563,2.854939,2.685266,3.34816
MD00G1002000,2.41494,2.463868,2.470049,2.613261,2.576815,2.296066,2.277826,2.382715,2.329795,2.857351,2.16088,2.585115,2.3057
MD00G1002100,1.856245,1.766623,2.192718,1.9758,1.372465,1.346592,1.294279,2.434389,2.401637,1.943977,2.171607,2.156644,1.889808
MD00G1002200,2.415919,2.234855,2.118146,2.487616,1.265053,1.655353,1.578375,1.438708,1.571695,1.564428,2.190602,2.621737,2.232404
MD00G1002500,1.794938,2.574585,2.19974,2.300694,2.203994,2.157548,2.21563,2.38745,1.942388,2.597048,2.321994,2.174149,1.843977
MD00G1002600,2.511032,2.147372,2.178689,2.033836,2.076008,1.957138,3.11344,2.450917,3.184336,2.385136,3.445098,2.460429,2.427365
MD00G1002700,2.466562,2.200628,2.402447,1.768002,2.576956,2.776423,2.992975,2.044115,3.389897,2.034527,3.470035,4.297166,2.281435
MD00G1002800,3.994084,3.585871,4.357335,4.134188,3.843827,4.029738,5.410013,4.366464,5.32427,5.007784,5.071291,4.958608,4.356433
MD00G1003400,2.028538,2.072182,2.080781,2.25311,2.311936,2.206668,2.107647,1.86438,1.809568,2.150551,2.07075,2.415351,2.620719
MD00G1003500,2.226612,1.528872,1.259334,1.752868,1.8164,1.521194,1.386067,1.855044,2.288861,1.823343,1.259023,1.369945,1.69697
MD00G1003600,1.073772,1.715179,2.027966,1.970396,2.462572,1.751237,2.013319,1.483089,1.99988,1.443287,2.069001,1.939983,1.855052
MD00G1003800,2.390463,2.873044,2.403015,2.404447,2.018727,2.537998,2.189413,2.712841,2.135105,2.285238,2.239648,2.636597,2.004905
MD00G1003900,1.703446,1.970978,1.510863,1.712658,1.421343,2.311724,1.868775,2.210896,1.416742,1.720507,1.567725,1.078489,1.795938
MD00G1004000,1.703446,1.970978,1.510863,1.712658,1.421343,2.311724,1.868775,2.210896,1.416742,1.720507,1.567725,1.078489,1.795938
MD00G1004100,2.077799,1.755617,1.755502,1.791851,1.969101,2.207733,1.756074,2.178037,1.699324,1.789315,1.634722,1.565095,2.105419
MD00G1004200,2.548076,2.641978,2.604369,2.44473,1.836607,1.962447,2.378719,2.61517,2.478992,2.56008,2.582974,1.634768,1.673753
MD00G1004300,1.612036,1.967232,2.218305,1.745579,1.786646,1.702544,2.079315,1.724835,2.201695,1.814631,2.220065,2.921447,2.336502
MD00G1004400,2.164274,3.437788,2.550175,2.197593,2.42354,2.774165,2.647565,2.981612,3.011943,2.766472,2.750117,2.558302,2.101304
MD00G1004500,1.562863,1.903747,2.025011,2.075749,1.698991,1.652251,1.96208,1.80638,1.656448,1.910941,1.64604,1.829799,1.917785
MD00G1004600,2.36317,2.503099,2.519259,2.03916,2.767873,2.993908,2.326631,2.839046,2.289534,2.543651,3.056814,2.689639,2.601197
MD00G1004800,3.746794,3.123988,2.949924,2.64992,3.968015,2.98616,3.333851,3.894271,3.01022,3.042386,2.751792,3.037028,3.027389
MD00G1004900,0.744066,1.259468,1.594375,1.389438,2.469316,1.81439,1.591478,1.645154,1.248302,1.567229,1.289813,2.03198,1.308723
MD00G1005000,2.446207,2.16673,2.163171,1.737868,1.730928,2.47845,1.943855,2.349324,1.893221,2.362094,2.214585,2.067912,2.039355
MD00G1005100,1.823199,1.870756,1.785622,1.598829,1.807607,2.47845,1.926293,2.349324,2.252178,2.396128,1.991982,2.009052,1.263667
MD00G1005200,2.111595,2.592773,2.939435,2.046883,2.610662,2.449314,2.522658,2.30789,2.099416,2.390972,2.144695,2.222533,1.97276
MD00G1005300,2.378513,2.274104,1.520462,1.867106,2.29072,1.683265,2.661895,1.787259,2.663831,1.965566,1.919959,2.427461,1.409311
MD00G1005400,1.795666,1.512733,1.729557,3.061003,2.663239,1.676437,1.718663,1.628097,1.612876,1.488433,1.971937,1.836687,1.375844
MD00G1005500,2.414038,1.919246,2.219146,2.210324,1.149259,2.171846,1.786743,2.66424,2.067954,2.454448,1.916486,1.586943,2.297859
MD00G1005600,1.936563,2.126083,2.094884,2.163891,2.223739,2.198092,2.253755,1.965388,1.720632,1.711622,2.191184,2.120873,2.703409
MD00G1005700,2.692422,2.898586,3.057661,2.272101,2.027973,3.116201,2.410556,2.850352,2.905121,2.369576,2.975354,2.014243,4.019969
MD00G1005800,5.520875,4.953854,5.028848,5.544439,4.229933,4.363564,4.949376,4.284729,4.164354,4.795535,5.658319,4.775579,6.228735
MD00G1006000,5.520875,4.953854,5.028848,5.544439,4.229933,4.363564,4.949376,4.284729,4.164354,4.795535,5.658319,4.775579,6.228735
MD00G1006100,6.541564,4.947242,5.200448,4.492183,3.998621,5.384482,3.978151,5.119616,5.70698,4.807953,6.375697,4.659516,5.1099
MD00G1006200,6.541564,4.947242,5.200448,4.492183,3.998621,5.384482,3.978151,5.119616,5.70698,4.807953,6.375697,4.659516,8.552848
MD00G1006300,5.348317,4.128381,4.878199,4.30267,3.177851,4.050224,3.129886,4.096313,3.39621,4.010886,5.052619,4.014279,8.552848
MD00G1006400,5.348317,4.128381,4.878199,4.30267,3.177851,4.050224,3.129886,4.096313,3.39621,4.010886,5.052619,4.014279,8.552848
MD00G1006500,1.440482,2.566236,0.558134,2.029866,1.265148,1.896924,2.408318,1.850964,1.507405,2.083132,2.162143,0.930414,1.825105
MD00G1006600,1.631539,2.227178,2.024415,1.953645,2.015661,1.135978,1.891613,1.14667,2.081705,0.979127,1.180121,1.18076,0.971039
MD00G1006700,2.553658,3.524931,3.890424,2.515227,3.32794,3.396594,2.562864,3.198709,2.875244,2.564198,3.54519,3.253588,4.183564
MD00G1006800,2.379107,2.518798,2.231753,2.385904,2.591147,2.463315,2.172921,2.369745,2.501216,2.492378,2.711549,2.421086,2.209753
MD00G1006900,2.355816,2.465554,2.303339,2.185439,3.029945,2.010026,2.206514,2.019717,2.033003,3.095664,2.405973,2.322713,2.149738
MD00G1007000,1.998491,2.162825,2.405373,2.565901,2.804743,2.893623,2.080854,2.410487,1.447073,2.550606,2.133352,1.831125,1.77128
MD00G1007100,1.487479,1.653466,1.585193,2.51545,1.723596,3.29495,1.867132,2.196815,1.964695,2.333356,1.236872,2.018299,1.543452
MD00G1007200,2.250107,2.035987,2.526968,2.450535,2.836576,3.23697,2.237378,3.11383,1.909359,2.876785,2.041528,1.857018,1.997909
MD00G1007300,2.568253,1.910426,2.947292,1.585057,2.429831,1.735305,2.288327,1.679089,2.473983,1.864545,2.109497,1.529249,2.154538
MD00G1007400,1.285421,1.145154,1.397188,1.114635,1.928633,1.592142,1.898336,1.889293,1.893778,1.838777,1.643816,1.346726,1.809133
MD00G1007500,1.285421,1.145154,1.397188,1.114635,1.928633,1.592142,1.898336,1.889293,1.893778,1.838777,1.643816,1.346726,1.809133
MD00G1007600,1.981502,1.698351,2.048078,1.835859,2.074079,1.887133,1.813438,1.369953,2.062317,2.064406,2.055993,1.618492,1.881864
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