diff --git a/Documentation/example_files/case_control/general/caco.paup b/Documentation/example_files/case_control/general/caco.paup new file mode 100644 index 0000000000000000000000000000000000000000..23125500521652fd5eb21c3576944d44ff9123db --- /dev/null +++ b/Documentation/example_files/case_control/general/caco.paup @@ -0,0 +1,38 @@ +#Nexus +Begin data; +dimension ntax=14 nchar=13; +format symbols="0123456789" missing=?; +matrix +H004_c002_m009 1122211111222 +H006_c003_m001 2222122222222 +H005_c004_m010 1122211121122 +H008_c011_m005 2222211111212 +H011_c002_m011 1122211122222 +H002_c006_m003 2222211222222 +H010_c013_m002 2211222222222 +H009_c006_m003 2212222222212 +[H001_c124_m095 2222222222222] +H003_c004_m018 1122222222222 +H014_c002_m003 2222211111122 +H013_c004_m010 1122211111212 +H007_c015_m028 1122211111122 +H012_c004_m002 2222211111222 +H000_ancetre 2222222222221 +; +end; +begin assumptions; +ancstates *anc vector = 2222222222221; +end; +begin paup; +set nowarnreset autoclose maxtrees = 1000 increase=no[ - Auto AutoInc = 100] monitor = no taxlabels = full +root=lundberg warnroot=no opt=deltran [- acctran] ancstates=anc; +hsearch; +savetrees from=1 to=1000 file=test.tree root=yes format=altnexus; +cleartrees nowarn=yes; +gettrees rooted=yes file=test.tree; +log file = test.res.log replace=yes [- no]; +describetrees all /plot=cladogram [- phylogram] brlens=yes rootmethod=lundberg apolist=yes; +log stop; +end; +quit; +[WARNING, this file is designed for bi-allelic data. If it is not the case, you may have to modify this input file, for example by specifying the ordered option in the typeset command in the assumption block] diff --git a/Documentation/example_files/case_control/general/caco.phase b/Documentation/example_files/case_control/general/caco.phase new file mode 100644 index 0000000000000000000000000000000000000000..aa8869fdc5a15d48ec57c1951cabf13fd65038ee --- /dev/null +++ b/Documentation/example_files/case_control/general/caco.phase @@ -0,0 +1,604 @@ +200 +12 +P 293 693 2319 2346 3697 3727 3848 4329 4384 4553 6297 6760 +SSSSSSSSSSSS +1 1 +222222222222 +222222222222 +1 2 +112221112222 +222222222222 +1 3 +222222222222 +112221111121 +1 4 +222222222222 +222222222222 +1 5 +112222222222 +221222222221 +1 6 +112222222222 +112221112222 +1 7 +112222222222 +222222222222 +1 8 +222222222222 +222222222222 +1 9 +222222222222 +112221111112 +1 10 +222222222222 +112221111122 +1 11 +112221111112 +112221111121 +1 12 +222222222222 +222221111112 +1 13 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+222222222222 +0 187 +222212222222 +221222222221 +0 188 +222222222222 +222222222222 +0 189 +222222222222 +112221111112 +0 190 +222222222222 +222222222222 +0 191 +222222222222 +112221111112 +0 192 +222222222222 +222221122222 +0 193 +221122222222 +112221111112 +0 194 +222222222222 +222222222222 +0 195 +222222222222 +222222222222 +0 196 +222222222222 +222221111121 +0 197 +222222222222 +112221112112 +0 198 +222221111121 +222212222222 +0 199 +222222222222 +222222222222 +0 200 +222222222222 +222222222222 diff --git a/Documentation/example_files/case_control/general/caco.phase.out b/Documentation/example_files/case_control/general/caco.phase.out new file mode 100644 index 0000000000000000000000000000000000000000..57cff6e7eeacb252e6576ea670e314353bc8834e --- /dev/null +++ b/Documentation/example_files/case_control/general/caco.phase.out @@ -0,0 +1,1673 @@ +************************************************************* +**** **** +**** Output from PHASE v2.0.2 **** +**** Code by M Stephens, with contributions from N Li **** +**** **** +************************************************************* + +BEGIN COMMAND_LINE +/home/cbardel/phase/phase.2.0.2.linux/PHASE -c-1 -MS caco.phase caco.out 100 1 100 +END COMMAND_LINE + +BEGIN OUTFILE_LIST +caco.out_freqs : haplotype frequency estimates +caco.out_pairs : most likely haplotype pairs for each individual +caco.out_signif : p-value for testing cases vs controls +caco.out_monitor : file for monitoring convergence +END OUTFILE_LIST + +BEGIN INPUT_SUMMARY +Number of Individuals: 200 +Number of Loci: 12 +Positions of loci: 293 693 2319 2346 3697 3727 3848 4329 4384 4553 6297 6760 +END INPUT_SUMMARY + +List of haplotypes found in best reconstruction, with counts. +(See file caco.out_freqs for haplotype population frequency estimates) + +BEGIN LIST_SUMMARY + 1 222222222222 219.000000 + 2 222221122222 9.000000 + 3 222221111122 6.000000 + 4 222221111121 16.000000 + 5 222221111112 5.000000 + 6 222212222222 4.000000 + 7 221222222221 9.000000 + 8 221122222222 15.000000 + 9 112222222222 22.000000 + 10 112221112222 13.000000 + 11 112221112112 14.000000 + 12 112221111122 11.000000 + 13 112221111121 14.000000 + 14 112221111112 43.000000 +END LIST_SUMMARY + + +Summary of best reconstruction +(numbers refer to the list of haplotypes given above) + +BEGIN BESTPAIRS_SUMMARY +1: (1,1) +2: (1,10) +3: (1,13) +4: (1,1) +5: (7,9) +6: (9,10) +7: (1,9) +8: (1,1) +9: (1,14) +10: (1,12) +11: (13,14) +12: (1,5) +13: (1,1) +14: (1,5) +15: (1,14) +16: (11,11) +17: (1,5) +18: (1,11) +19: (1,14) +20: (1,10) +21: (1,12) +22: (1,10) +23: (9,14) +24: (1,14) +25: (1,9) +26: (1,14) +27: (8,12) +28: (1,9) +29: (1,1) +30: (1,2) +31: (9,10) +32: (1,1) +33: (1,9) +34: (9,11) +35: (1,2) +36: (1,14) +37: (1,13) +38: (1,13) +39: (1,2) +40: (12,14) +41: (1,12) +42: (1,9) +43: (1,1) +44: (1,4) +45: (1,1) +46: (9,14) +47: (14,14) +48: (1,11) +49: (1,10) +50: (1,14) +51: (3,4) +52: (1,14) +53: (1,14) +54: (1,14) +55: (1,1) +56: (1,13) +57: (1,8) +58: 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1 1 1 = = = = +1 99 +2 2 = = = 2 2 2 2 2 = = +1 1 = = = 1 1 1 1 1 = = +1 100 +2 2 = = 1 2 2 2 2 2 2 = +1 1 = = 2 1 1 1 1 1 1 = +0 101 += = = = = = = = = = = = += = = = = = = = = = = = +0 102 +2 2 = = = 2 2 2 = 2 2 = +1 1 = = = 1 1 1 = 1 1 = +0 103 +2 2 = = = 2 2 2 = 2 2 = +1 1 = = = 1 1 1 = 1 1 = +0 104 += = = = = 2 2 2 2 2 = = += = = = = 1 1 1 1 1 = = +0 105 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 106 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 107 += = = = = = = = = = = = += = = = = = = = = = = = +0 108 += = = = = = = = = = = = += = = = = = = = = = = = +0 109 += = = = = 2 2 2 2 2 = 2 += = = = = 1 1 1 1 1 = 1 +0 110 += = = = = = = = = = = = += = = = = = = = = = = = +0 111 += = = = = = = = = = = = += = = = = = = = = = = = +0 112 += = = = = = = = = = = = += = = = = = = = = = = = +0 113 += = = = = 2 2 2 2 2 = 2 += = = = = 1 1 1 1 1 = 1 +0 114 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 115 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 116 += = = = = = = = = = = = += = = = = = = = = = = = +0 117 += = 2 2 = 1 1 = = = = = += = 1 1 = 2 2 = = = = = +0 118 += = = = = = = = = = = = += = = = = = = = = = = = +0 119 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 120 += = = = = 2 2 2 2 2 2 = += = = = = 1 1 1 1 1 1 = +0 121 += = = = = 2 2 2 2 2 = 2 += = = = = 1 1 1 1 1 = 1 +0 122 += = = = = = = = = = = = += = = = = = = = = = = = +0 123 +2 2 1 = = = = = = = = 1 +1 1 2 = = = = = = = = 2 +0 124 += = 2 = = 1 1 1 1 1 1 2 += = 1 = = 2 2 2 2 2 2 1 +0 125 +2 2 = = 1 2 2 2 2 2 2 = +1 1 = = 2 1 1 1 1 1 1 = +0 126 += = = = = = = = = = = = += = = = = = = = = = = = +0 127 += = = = = 2 2 = = = = = += = = = = 1 1 = = = = = +0 128 += = = = = = = = = = = = += = = = = = = = = = = = +0 129 += = = = = = = = = = = = += = = = = = = = = = = = +0 130 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 131 += = = = = = = = = = = = += = = = = = = = = = = = +0 132 += = 2 = = = = = = = = 2 += = 1 = = = = = = = = 1 +0 133 += = = = = 2 2 2 2 2 = 2 += = = = = 1 1 1 1 1 = 1 +0 134 += = = = = 2 2 2 2 2 = 2 += = = = = 1 1 1 1 1 = 1 +0 135 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 136 += = = = = 2 2 = = = = = += = = = = 1 1 = = = = = +0 137 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 138 +(2) (2) = = = 2 2 2 2 2 = 2 +(1) (1) = = = 1 1 1 1 1 = 1 +0 139 += = = = = = = = = = = = += = = = = = = = = = = = +0 140 += = = = = = = = = = = = += = = = = = = = = = = = +0 141 += = = = = = = = = = = = += = = = = = = = = = = = +0 142 += = = = = = = = = = = = += = = = = = = = = = = = +0 143 +2 2 = = = = = 2 2 2 = 2 +1 1 = = = = = 1 1 1 = 1 +0 144 += = 2 2 = 1 1 1 1 1 = 1 += = 1 1 = 2 2 2 2 2 = 2 +0 145 += = = = = = = = = = = = += = = = = = = = = = = = +0 146 += = = = = = = = = = = = += = = = = = = = = = = = +0 147 += = = = = = = = = = = = += = = = = = = = = = = = +0 148 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 149 += = = = = = = = = = = = += = = = = = = = = = = = +0 150 +(2) (2) = = = 2 2 2 2 2 = 2 +(1) (1) = = = 1 1 1 1 1 = 1 +0 151 +2 2 = = = = = = 1 1 = = +1 1 = = = = = = 2 2 = = +0 152 += = = = = 2 2 2 2 2 = 2 += = = = = 1 1 1 1 1 = 1 +0 153 += = = = = = = = = = = = += = = = = = = = = = = = +0 154 += = 2 = = 1 1 1 1 1 = 2 += = 1 = = 2 2 2 2 2 = 1 +0 155 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 156 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 157 += = = = = 2 2 2 2 2 = 2 += = = = = 1 1 1 1 1 = 1 +0 158 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 159 += = = = = = = = = = = = += = = = = = = = = = = = +0 160 += = = = = 2 2 = = = = = += = = = = 1 1 = = = = = +0 161 += = = = = = = = = = = = += = = = = = = = = = = = +0 162 +2 2 = = = 2 2 2 = 2 2 = +1 1 = = = 1 1 1 = 1 1 = +0 163 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 164 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 165 += = = = = = = = = = = = += = = = = = = = = = = = +0 166 += = = = = = = = = = = = += = = = = = = = = = = = +0 167 += = = = = = = = = = = = += = = = = = = = = = = = +0 168 +2 2 1 = = 2 2 2 2 2 = 1 +1 1 2 = = 1 1 1 1 1 = 2 +0 169 += = = = = 2 2 2 = = = = += = = = = 1 1 1 = = = = +0 170 += = = = = = = = = = = = += = = = = = = = = = = = +0 171 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 172 += = = = = = = = = = = = += = = = = = = = = = = = +0 173 +2 2 = = = 2 2 2 2 2 = = +1 1 = = = 1 1 1 1 1 = = +0 174 += = = = = = = = = = = = += = = = = = = = = = = = +0 175 += = = = = 2 2 2 2 2 = = += = = = = 1 1 1 1 1 = = +0 176 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 177 += = = = = = = = = = = = += = = = = = = = = = = = +0 178 += = = = = = = = = = = = += = = = = = = = = = = = +0 179 +2 2 = = = = = = = = = = +1 1 = = = = = = = = = = +0 180 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 181 += = = = = = = = = = = = += = = = = = = = = = = = +0 182 += = = = = = = = = = = = += = = = = = = = = = = = +0 183 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 184 += = 2 2 = = = = = = = = += = 1 1 = = = = = = = = +0 185 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 186 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 187 += = 2 = 1 = = = = = = 2 += = 1 = 2 = = = = = = 1 +0 188 += = = = = = = = = = = = += = = = = = = = = = = = +0 189 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 190 += = = = = = = = = = = = += = = = = = = = = = = = +0 191 +2 2 = = = 2 2 2 2 2 2 = +1 1 = = = 1 1 1 1 1 1 = +0 192 += = = = = 2 2 = = = = = += = = = = 1 1 = = = = = +0 193 +2 2 1 1 = 2 2 2 2 2 2 = +1 1 2 2 = 1 1 1 1 1 1 = +0 194 += = = = = = = = = = = = += = = = = = = = = = = = +0 195 += = = = = = = = = = = = += = = = = = = = = = = = +0 196 += = = = = 2 2 2 2 2 = 2 += = = = = 1 1 1 1 1 = 1 +0 197 +2 2 = = = 2 2 2 = 2 2 = +1 1 = = = 1 1 1 = 1 1 = +0 198 += = = = 2 1 1 1 1 1 = 1 += = = = 1 2 2 2 2 2 = 2 +0 199 += = = = = = = = = = = = += = = = = = = = = = = = +0 200 += = = = = = = = = = = = += = = = = = = = = = = = +END BESTPAIRS2 + + +Phase probabilities at each site +with phase known positions indicated by = +and missing data positions indicated by ? + +BEGIN PHASEPROBS += = = = = = = = = = = = +1.00 1.00 = = = 1.00 1.00 1.00 = = = = +0.87 0.87 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = = = = = = = = +1.00 1.00 1.00 = = = = = = = = 1.00 += = = = = 1.00 1.00 1.00 = = = = +1.00 1.00 = = = = = = = = = = += = = = = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.93 0.93 = = = 1.00 1.00 1.00 1.00 1.00 = = += = = = = = = = = = 1.00 1.00 += = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +1.00 1.00 = = = 1.00 1.00 1.00 = = = = +0.93 0.93 = = = 1.00 1.00 1.00 1.00 1.00 = = +1.00 1.00 = = = 1.00 1.00 1.00 = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +1.00 1.00 = = = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = = +1.00 1.00 = = = = = = = = = = += = = = = = = = = = = = += = = = = 1.00 1.00 = = = = = += = = = = 1.00 1.00 1.00 = = = = += = = = = = = = = = = = +1.00 1.00 = = = = = = = = = = += = = = = 1.00 1.00 1.00 = 1.00 1.00 = += = = = = 1.00 1.00 = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.86 0.86 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 +0.86 0.86 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = 1.00 1.00 = = = = = += = = = = = = = = = 1.00 = +0.93 0.93 = = = 1.00 1.00 1.00 1.00 1.00 = = +1.00 1.00 = = = = = = = = = = += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = +1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = +1.00 1.00 = = = 1.00 1.00 1.00 = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = 1.00 +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = +0.86 0.86 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = 1.00 1.00 = = = = = = = = +0.90 0.90 = = = = = = = = 1.00 1.00 +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 +1.00 1.00 = = = = = = = = = = +0.86 0.86 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +1.00 1.00 = = = = = = 1.00 = 1.00 1.00 += = = = = = = = 1.00 = 1.00 = +0.93 0.93 = = = 1.00 1.00 1.00 1.00 1.00 = = +1.00 1.00 = = = = = = = = = = += = = = = = = = = 1.00 1.00 = += = = = = = = = = = = = +1.00 1.00 = = = = = = = = = = += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 = = = = +0.86 0.86 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 +1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = 1.00 = = = = = = = = 1.00 += = = = = = = = = = = = += = = = = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = 1.00 = = = = = = = = 1.00 += = = = = = = = = = = = += = = = = = = = 1.00 1.00 1.00 = +0.87 0.87 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = = = = = = = = +0.89 0.89 = = = = = = = = 1.00 1.00 += = = = = 1.00 1.00 1.00 1.00 1.00 = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = +1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = += = = = = = = = 1.00 1.00 = 1.00 += = = = = = = = = = = = += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 = = +1.00 1.00 = = = 1.00 1.00 1.00 = = = = +0.93 0.93 = = = 1.00 1.00 1.00 1.00 1.00 = = +1.00 1.00 = = 0.92 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = +1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = +1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = += = = = = 1.00 1.00 1.00 1.00 1.00 = = += = 1.00 1.00 = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = = = = = = = = += = = = = = = = = = = = += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = += = 1.00 1.00 = 1.00 1.00 = = = = = += = = = = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = = = = = = = = +1.00 1.00 1.00 = = = = = = = = 1.00 += = 1.00 = = 1.00 1.00 1.00 1.00 1.00 1.00 1.00 +1.00 1.00 = = 0.93 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = += = = = = 1.00 1.00 = = = = = += = = = = = = = = = = = += = = = = = = = = = = = += = 1.00 1.00 = = = = = = = = += = = = = = = = = = = = += = 1.00 = = = = = = = = 1.00 += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = 1.00 1.00 = = = = = = = = += = = = = 1.00 1.00 = = = = = += = 1.00 1.00 = = = = = = = = +0.86 0.86 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = = = = = = = = += = = = = = = = = = = = += = = = = = = = = = = = += = = = = = = = = = = = +1.00 1.00 = = = = = 1.00 1.00 1.00 = 1.00 += = 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = = = = = = = = += = = = = = = = = = = = += = = = = = = = = = = = += = 1.00 1.00 = = = = = = = = += = = = = = = = = = = = +0.86 0.86 = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 +1.00 1.00 = = = = = = 1.00 1.00 = = += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = = = = = = = = += = 0.97 = = 1.00 1.00 1.00 1.00 1.00 = 0.93 +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = 1.00 1.00 = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 += = 1.00 1.00 = = = = = = = = += = = = = = = = = = = = += = = = = 1.00 1.00 = = = = = += = = = = = = = = = = = +1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = += = = = = = = = = = = = += = = = = = = = = = = = +1.00 1.00 0.98 = = 1.00 1.00 1.00 1.00 1.00 = 0.95 += = = = = 1.00 1.00 1.00 = = = = += = = = = = = = = = = = += = 1.00 1.00 = = = = = = = = += = = = = = = = = = = = +0.93 0.93 = = = 1.00 1.00 1.00 1.00 1.00 = = += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = += = = = = = = = = = = = +1.00 1.00 = = = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = += = = = = = = = = = = = += = 1.00 1.00 = = = = = = = = += = 1.00 1.00 = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = 1.00 = 0.96 = = = = = = 1.00 += = = = = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = +0.98 0.98 = = = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = 1.00 1.00 = = = = = +1.00 1.00 1.00 1.00 = 1.00 1.00 1.00 1.00 1.00 1.00 = += = = = = = = = = = = = += = = = = = = = = = = = += = = = = 1.00 1.00 1.00 1.00 1.00 = 1.00 +1.00 1.00 = = = 1.00 1.00 1.00 = 1.00 1.00 = += = = = 0.97 1.00 1.00 1.00 1.00 1.00 = 1.00 += = = = = = = = = = = = += = = = = = = = = = = = +END PHASEPROBS diff --git a/Documentation/example_files/case_control/general/caco.prepaup b/Documentation/example_files/case_control/general/caco.prepaup new file mode 100644 index 0000000000000000000000000000000000000000..24960588c65ee26a477af1db87658717bf27adf8 --- /dev/null +++ b/Documentation/example_files/case_control/general/caco.prepaup @@ -0,0 +1,38 @@ +#Nexus +Begin data; +dimension ntax=15 nchar=13; +format symbols="0123456789" missing=?; +matrix +H004_c002_m009 1122211111222 +H006_c003_m001 2222122222222 +H005_c004_m010 1122211121122 +H008_c011_m005 2222211111212 +H011_c002_m011 1122211122222 +H002_c006_m003 2222211222222 +H010_c013_m002 2211222222222 +H009_c006_m003 2212222222212 +H001_c124_m095 2222222222222 +H003_c004_m018 1122222222222 +H014_c002_m003 2222211111122 +H013_c004_m010 1122211111212 +H007_c015_m028 1122211111122 +H012_c004_m002 2222211111222 +H000_ancetre [add ancestral haplotype]1 +; +end; +begin assumptions; +ancstates *anc vector = [add ancestral haplotype]1; +end; +begin paup; +set nowarnreset autoclose maxtrees = [2000] increase=[no - Auto AutoInc = 100] monitor = no taxlabels = full +root=lundberg warnroot=no opt=[deltran - acctran] ancstates=anc; +hsearch; +savetrees [from=1 to=1] file=[test.tree] root=yes format=altnexus; +cleartrees nowarn=yes; +gettrees rooted=yes file=[test.tree]; +log file = [test.res.log] replace=[yes - no]; +describetrees [all] /plot=[cladogram - phylogram] brlens=yes rootmethod=lundberg apolist=yes; +log stop; +end; +quit; +[WARNING, this file is designed for bi-allelic data. If it is not the case, you may have to modify this input file, for example by specifying the ordered option in the typeset command in the assumption block]