forester/aptx/aptx_example_files/apaf.xml

   1 <?xml version="1.0" encoding="UTF-8"?>
   2 <phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
   3    xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd"
   4    xmlns="http://www.phyloxml.org">
   5    <phylogeny rooted="true">
   6       <clade>
   7          <clade>
   8             <branch_length>0.18105</branch_length>
   9             <confidence type="unknown">89.0</confidence>
  10             <clade>
  11                <branch_length>0.07466</branch_length>
  12                <confidence type="unknown">32.0</confidence>
  13                <clade>
  14                   <branch_length>0.26168</branch_length>
  15                   <confidence type="unknown">100.0</confidence>
  16                   <clade>
  17                      <branch_length>0.22058</branch_length>
  18                      <confidence type="unknown">89.0</confidence>
  19                      <clade>
  20                         <branch_length>0.28901</branch_length>
  21                         <confidence type="unknown">100.0</confidence>
  22                         <clade>
  23                            <branch_length>0.06584</branch_length>
  24                            <confidence type="unknown">100.0</confidence>
  25                            <clade>
  26                               <branch_length>0.02309</branch_length>
  27                               <confidence type="unknown">43.0</confidence>
  28                               <clade>
  29                                  <branch_length>0.0746</branch_length>
  30                                  <confidence type="unknown">100.0</confidence>
  31                                  <clade>
  32                                     <branch_length>0.02365</branch_length>
  33                                     <confidence type="unknown">88.0</confidence>
  34                                     <clade>
  35                                        <name>22_MOUSE</name>
  36                                        <branch_length>0.05998</branch_length>
  37                                        <taxonomy>
  38                                           <code>MOUSE</code>
  39                                        </taxonomy>
  40                                        <sequence>
  41                                           <domain_architecture length="1249">
  42                                              <domain from="6" to="90" confidence="7.0E-26">CARD</domain>
  43                                              <domain from="109" to="414" confidence="7.2E-117">NB-ARC</domain>
  44                                              <domain from="605" to="643" confidence="2.4E-6">WD40</domain>
  45                                              <domain from="647" to="685" confidence="1.1E-12">WD40</domain>
  46                                              <domain from="689" to="729" confidence="2.4E-7">WD40</domain>
  47                                              <domain from="733" to="771" confidence="4.7E-14">WD40</domain>
  48                                              <domain from="872" to="910" confidence="2.5E-8">WD40</domain>
  49                                              <domain from="993" to="1031" confidence="4.6E-6">WD40</domain>
  50                                              <domain from="1075" to="1113" confidence="6.3E-7">WD40</domain>
  51                                              <domain from="1117" to="1155" confidence="1.4E-7">WD40</domain>
  52                                              <domain from="1168" to="1204" confidence="0.3">WD40</domain>
  53                                           </domain_architecture>
  54                                        </sequence>
  55                                     </clade>
  56                                     <clade>
  57                                        <name>Apaf-1_HUMAN</name>
  58                                        <branch_length>0.01825</branch_length>
  59                                        <taxonomy>
  60                                           <code>HUMAN</code>
  61                                        </taxonomy>
  62                                        <sequence>
  63                                           <domain_architecture length="1248">
  64                                              <domain from="6" to="90" confidence="1.1E-25">CARD</domain>
  65                                              <domain from="109" to="414" confidence="3.0E-134">NB-ARC</domain>
  66                                              <domain from="605" to="643" confidence="8.5E-6">WD40</domain>
  67                                              <domain from="647" to="685" confidence="2.5E-11">WD40</domain>
  68                                              <domain from="689" to="729" confidence="2.4E-8">WD40</domain>
  69                                              <domain from="733" to="771" confidence="3.6E-14">WD40</domain>
  70                                              <domain from="872" to="910" confidence="3.8E-8">WD40</domain>
  71                                              <domain from="1075" to="1113" confidence="4.0E-7">WD40</domain>
  72                                              <domain from="1117" to="1155" confidence="5.9E-8">WD40</domain>
  73                                           </domain_architecture>
  74                                        </sequence>
  75                                     </clade>
  76                                  </clade>
  77                                  <clade>
  78                                     <name>12_CANFA</name>
  79                                     <branch_length>0.04683</branch_length>
  80                                     <taxonomy>
  81                                        <code>CANFA</code>
  82                                     </taxonomy>
  83                                     <sequence>
  84                                        <domain_architecture length="1153">
  85                                           <domain from="6" to="90" confidence="4.5E-22">CARD</domain>
  86                                           <domain from="110" to="415" confidence="4.0E-119">NB-ARC</domain>
  87                                           <domain from="597" to="635" confidence="3.9E-5">WD40</domain>
  88                                           <domain from="639" to="677" confidence="2.5E-11">WD40</domain>
  89                                           <domain from="681" to="721" confidence="1.8E-7">WD40</domain>
  90                                           <domain from="725" to="763" confidence="9.4E-13">WD40</domain>
  91                                           <domain from="889" to="927" confidence="1.1E-6">WD40</domain>
  92                                           <domain from="971" to="1009" confidence="1.7E-7">WD40</domain>
  93                                           <domain from="1013" to="1051" confidence="1.9E-7">WD40</domain>
  94                                        </domain_architecture>
  95                                     </sequence>
  96                                  </clade>
  97                               </clade>
  98                               <clade>
  99                                  <name>11_CHICK</name>
 100                                  <branch_length>0.15226</branch_length>
 101                                  <taxonomy>
 102                                     <code>CHICK</code>
 103                                  </taxonomy>
 104                                  <sequence>
 105                                     <domain_architecture length="1207">
 106                                        <domain from="6" to="90" confidence="3.6E-21">CARD</domain>
 107                                        <domain from="109" to="414" confidence="3.6E-109">NB-ARC</domain>
 108                                        <domain from="603" to="641" confidence="1.6E-4">WD40</domain>
 109                                        <domain from="645" to="683" confidence="8.2E-11">WD40</domain>
 110                                        <domain from="687" to="727" confidence="6.2E-10">WD40</domain>
 111                                        <domain from="731" to="769" confidence="1.8E-11">WD40</domain>
 112                                        <domain from="828" to="866" confidence="1.8">WD40</domain>
 113                                        <domain from="993" to="1030" confidence="2.9E-4">WD40</domain>
 114                                        <domain from="1034" to="1072" confidence="1.7E-8">WD40</domain>
 115                                        <domain from="1076" to="1114" confidence="7.5E-9">WD40</domain>
 116                                        <domain from="1127" to="1163" confidence="0.044">WD40</domain>
 117                                     </domain_architecture>
 118                                  </sequence>
 119                               </clade>
 120                            </clade>
 121                            <clade>
 122                               <name>16_XENLA</name>
 123                               <branch_length>0.4409</branch_length>
 124                               <taxonomy>
 125                                  <code>XENLA</code>
 126                               </taxonomy>
 127                               <sequence>
 128                                  <domain_architecture length="1362">
 129                                     <domain from="6" to="90" confidence="4.0E-20">CARD</domain>
 130                                     <domain from="109" to="410" confidence="3.1E-56">NB-ARC</domain>
 131                                     <domain from="148" to="298" confidence="0.8">NACHT</domain>
 132                                     <domain from="729" to="767" confidence="7.0E-6">WD40</domain>
 133                                     <domain from="771" to="809" confidence="2.3E-11">WD40</domain>
 134                                     <domain from="813" to="853" confidence="1.1E-8">WD40</domain>
 135                                     <domain from="857" to="895" confidence="1.1E-10">WD40</domain>
 136                                     <domain from="992" to="1030" confidence="8.4E-9">WD40</domain>
 137                                     <domain from="1116" to="1154" confidence="7.3E-11">WD40</domain>
 138                                     <domain from="1158" to="1196" confidence="1.6E-8">WD40</domain>
 139                                     <domain from="1200" to="1238" confidence="1.2E-7">WD40</domain>
 140                                  </domain_architecture>
 141                               </sequence>
 142                            </clade>
 143                         </clade>
 144                         <clade>
 145                            <branch_length>0.17031</branch_length>
 146                            <confidence type="unknown">100.0</confidence>
 147                            <clade>
 148                               <branch_length>0.10929</branch_length>
 149                               <confidence type="unknown">100.0</confidence>
 150                               <clade>
 151                                  <name>14_FUGRU</name>
 152                                  <branch_length>0.02255</branch_length>
 153                                  <taxonomy>
 154                                     <code>FUGRU</code>
 155                                  </taxonomy>
 156                                  <sequence>
 157                                     <domain_architecture length="1258">
 158                                        <domain from="8" to="92" confidence="4.6E-24">CARD</domain>
 159                                        <domain from="111" to="418" confidence="7.0E-74">NB-ARC</domain>
 160                                        <domain from="609" to="647" confidence="2.8E-4">WD40</domain>
 161                                        <domain from="651" to="689" confidence="2.3E-12">WD40</domain>
 162                                        <domain from="740" to="778" confidence="1.8E-6">WD40</domain>
 163                                        <domain from="874" to="912" confidence="1.6E-9">WD40</domain>
 164                                        <domain from="998" to="1036" confidence="9.8E-13">WD40</domain>
 165                                        <domain from="1040" to="1080" confidence="1.6E-4">WD40</domain>
 166                                        <domain from="1084" to="1122" confidence="1.5E-9">WD40</domain>
 167                                        <domain from="1126" to="1164" confidence="6.2E-9">WD40</domain>
 168                                     </domain_architecture>
 169                                  </sequence>
 170                               </clade>
 171                               <clade>
 172                                  <name>15_TETNG</name>
 173                                  <branch_length>0.09478</branch_length>
 174                                  <taxonomy>
 175                                     <code>TETNG</code>
 176                                  </taxonomy>
 177                                  <sequence>
 178                                     <domain_architecture length="621">
 179                                        <domain from="8" to="92" confidence="2.5E-24">CARD</domain>
 180                                        <domain from="104" to="308" confidence="9.8E-11">NB-ARC</domain>
 181                                        <domain from="366" to="404" confidence="1.2E-12">WD40</domain>
 182                                        <domain from="455" to="493" confidence="1.0E-10">WD40</domain>
 183                                        <domain from="537" to="575" confidence="4.1E-10">WD40</domain>
 184                                     </domain_architecture>
 185                                  </sequence>
 186                               </clade>
 187                            </clade>
 188                            <clade>
 189                               <name>17_BRARE</name>
 190                               <branch_length>0.1811</branch_length>
 191                               <taxonomy>
 192                                  <code>BRARE</code>
 193                               </taxonomy>
 194                               <sequence>
 195                                  <domain_architecture length="1260">
 196                                     <domain from="6" to="90" confidence="3.9E-23">CARD</domain>
 197                                     <domain from="137" to="444" confidence="1.7E-72">NB-ARC</domain>
 198                                     <domain from="635" to="673" confidence="1.6">WD40</domain>
 199                                     <domain from="694" to="732" confidence="5.3E-12">WD40</domain>
 200                                     <domain from="783" to="821" confidence="2.0E-8">WD40</domain>
 201                                     <domain from="1040" to="1078" confidence="2.4E-8">WD40</domain>
 202                                     <domain from="1081" to="1121" confidence="6.6E-4">WD40</domain>
 203                                     <domain from="1125" to="1163" confidence="5.1E-8">WD40</domain>
 204                                     <domain from="1167" to="1205" confidence="1.3E-7">WD40</domain>
 205                                  </domain_architecture>
 206                               </sequence>
 207                            </clade>
 208                         </clade>
 209                      </clade>
 210                      <clade>
 211                         <branch_length>0.01594</branch_length>
 212                         <confidence type="unknown">53.0</confidence>
 213                         <clade>
 214                            <branch_length>0.10709</branch_length>
 215                            <confidence type="unknown">68.0</confidence>
 216                            <clade>
 217                               <name>1_BRAFL</name>
 218                               <branch_length>0.26131</branch_length>
 219                               <taxonomy>
 220                                  <code>BRAFL</code>
 221                               </taxonomy>
 222                               <sequence>
 223                                  <domain_architecture length="1238">
 224                                     <domain from="6" to="89" confidence="5.7E-19">CARD</domain>
 225                                     <domain from="111" to="413" confidence="4.2E-48">NB-ARC</domain>
 226                                     <domain from="600" to="638" confidence="3.2E-8">WD40</domain>
 227                                     <domain from="642" to="680" confidence="1.5E-10">WD40</domain>
 228                                     <domain from="730" to="768" confidence="9.6E-11">WD40</domain>
 229                                     <domain from="857" to="895" confidence="3.7E-10">WD40</domain>
 230                                     <domain from="984" to="1022" confidence="6.7E-10">WD40</domain>
 231                                     <domain from="1025" to="1064" confidence="3.1E-6">WD40</domain>
 232                                     <domain from="1069" to="1107" confidence="1.5E-4">WD40</domain>
 233                                     <domain from="1111" to="1149" confidence="7.9E-7">WD40</domain>
 234                                  </domain_architecture>
 235                               </sequence>
 236                            </clade>
 237                            <clade>
 238                               <name>18_NEMVE</name>
 239                               <branch_length>0.38014</branch_length>
 240                               <taxonomy>
 241                                  <code>NEMVE</code>
 242                               </taxonomy>
 243                               <sequence>
 244                                  <domain_architecture length="1290">
 245                                     <domain from="7" to="90" confidence="1.5E-13">CARD</domain>
 246                                     <domain from="117" to="200" confidence="5.4E-14">CARD</domain>
 247                                     <domain from="216" to="517" confidence="1.5E-50">NB-ARC</domain>
 248                                     <domain from="711" to="749" confidence="1.0E-7">WD40</domain>
 249                                     <domain from="753" to="791" confidence="8.5E-12">WD40</domain>
 250                                     <domain from="795" to="833" confidence="4.3E-11">WD40</domain>
 251                                     <domain from="837" to="875" confidence="1.0E-12">WD40</domain>
 252                                     <domain from="920" to="957" confidence="2.0E-4">WD40</domain>
 253                                     <domain from="961" to="999" confidence="3.0E-6">WD40</domain>
 254                                     <domain from="1085" to="1123" confidence="4.4E-6">WD40</domain>
 255                                     <domain from="1128" to="1166" confidence="3.0E-4">WD40</domain>
 256                                     <domain from="1170" to="1207" confidence="1.7E-10">WD40</domain>
 257                                  </domain_architecture>
 258                               </sequence>
 259                            </clade>
 260                         </clade>
 261                         <clade>
 262                            <name>23_STRPU</name>
 263                            <branch_length>0.48179</branch_length>
 264                            <taxonomy>
 265                               <code>STRPU</code>
 266                            </taxonomy>
 267                            <sequence>
 268                               <domain_architecture length="1236">
 269                                  <domain from="110" to="402" confidence="1.0E-40">NB-ARC</domain>
 270                                  <domain from="594" to="632" confidence="8.9E-4">WD40</domain>
 271                                  <domain from="636" to="673" confidence="2.5E-6">WD40</domain>
 272                                  <domain from="721" to="759" confidence="0.0043">WD40</domain>
 273                                  <domain from="765" to="802" confidence="0.0036">WD40</domain>
 274                                  <domain from="848" to="886" confidence="9.0E-10">WD40</domain>
 275                                  <domain from="975" to="1013" confidence="1.9E-5">WD40</domain>
 276                                  <domain from="1015" to="1053" confidence="2.4E-6">WD40</domain>
 277                                  <domain from="1057" to="1095" confidence="2.7E-9">WD40</domain>
 278                                  <domain from="1099" to="1137" confidence="4.9E-8">WD40</domain>
 279                                  <domain from="1141" to="1177" confidence="0.011">WD40</domain>
 280                               </domain_architecture>
 281                            </sequence>
 282                         </clade>
 283                      </clade>
 284                   </clade>
 285                   <clade>
 286                      <branch_length>0.34475</branch_length>
 287                      <confidence type="unknown">100.0</confidence>
 288                      <clade>
 289                         <name>26_STRPU</name>
 290                         <branch_length>0.36374</branch_length>
 291                         <taxonomy>
 292                            <code>STRPU</code>
 293                         </taxonomy>
 294                         <sequence>
 295                            <domain_architecture length="1319">
 296                               <domain from="18" to="98" confidence="3.4E-5">Death</domain>
 297                               <domain from="189" to="481" confidence="1.8E-10">NB-ARC</domain>
 298                               <domain from="630" to="668" confidence="8.2E-5">WD40</domain>
 299                            </domain_architecture>
 300                         </sequence>
 301                      </clade>
 302                      <clade>
 303                         <name>25_STRPU</name>
 304                         <branch_length>0.33137</branch_length>
 305                         <taxonomy>
 306                            <code>STRPU</code>
 307                         </taxonomy>
 308                         <sequence>
 309                            <domain_architecture length="1947">
 310                               <domain from="143" to="227" confidence="7.4E-5">Death</domain>
 311                               <domain from="227" to="550" confidence="2.0E-13">NB-ARC</domain>
 312                               <domain from="697" to="736" confidence="7.9E-4">WD40</domain>
 313                               <domain from="745" to="785" confidence="1.5">WD40</domain>
 314                               <domain from="1741" to="1836" confidence="2.0">Adeno_VII</domain>
 315                            </domain_architecture>
 316                         </sequence>
 317                      </clade>
 318                   </clade>
 319                </clade>
 320                <clade>
 321                   <branch_length>1.31498</branch_length>
 322                   <confidence type="unknown">100.0</confidence>
 323                   <clade>
 324                      <name>CED4_CAEEL</name>
 325                      <branch_length>0.13241</branch_length>
 326                      <taxonomy>
 327                         <code>CAEEL</code>
 328                      </taxonomy>
 329                      <sequence>
 330                         <domain_architecture length="714">
 331                            <domain from="7" to="90" confidence="9.2E-14">CARD</domain>
 332                            <domain from="116" to="442" confidence="5.8E-151">NB-ARC</domain>
 333                         </domain_architecture>
 334                      </sequence>
 335                   </clade>
 336                   <clade>
 337                      <name>31_CAEBR</name>
 338                      <branch_length>0.04777</branch_length>
 339                      <taxonomy>
 340                         <code>CAEBR</code>
 341                      </taxonomy>
 342                      <sequence>
 343                         <domain_architecture length="554">
 344                            <domain from="1" to="75" confidence="0.0046">CARD</domain>
 345                            <domain from="101" to="427" confidence="2.1E-123">NB-ARC</domain>
 346                         </domain_architecture>
 347                      </sequence>
 348                   </clade>
 349                </clade>
 350             </clade>
 351             <clade>
 352                <branch_length>0.13172</branch_length>
 353                <confidence type="unknown">45.0</confidence>
 354                <clade>
 355                   <branch_length>0.24915</branch_length>
 356                   <confidence type="unknown">95.0</confidence>
 357                   <clade>
 358                      <branch_length>0.76898</branch_length>
 359                      <confidence type="unknown">100.0</confidence>
 360                      <clade>
 361                         <name>28_DROPS</name>
 362                         <branch_length>0.1732</branch_length>
 363                         <taxonomy>
 364                            <code>DROPS</code>
 365                         </taxonomy>
 366                         <sequence>
 367                            <domain_architecture length="535">
 368                               <domain from="112" to="399" confidence="1.4E-5">NB-ARC</domain>
 369                            </domain_architecture>
 370                         </sequence>
 371                      </clade>
 372                      <clade>
 373                         <name>Dark_DROME</name>
 374                         <branch_length>0.18863</branch_length>
 375                         <taxonomy>
 376                            <code>DROME</code>
 377                         </taxonomy>
 378                         <sequence>
 379                            <domain_architecture length="1421">
 380                               <domain from="108" to="397" confidence="2.1E-5">NB-ARC</domain>
 381                            </domain_architecture>
 382                         </sequence>
 383                      </clade>
 384                   </clade>
 385                   <clade>
 386                      <name>29_AEDAE</name>
 387                      <branch_length>0.86398</branch_length>
 388                      <taxonomy>
 389                         <code>AEDAE</code>
 390                      </taxonomy>
 391                      <sequence>
 392                         <domain_architecture length="423">
 393                            <domain from="109" to="421" confidence="9.3E-6">NB-ARC</domain>
 394                         </domain_architecture>
 395                      </sequence>
 396                   </clade>
 397                </clade>
 398                <clade>
 399                   <name>30_TRICA</name>
 400                   <branch_length>0.97698</branch_length>
 401                   <taxonomy>
 402                      <code>TRICA</code>
 403                   </taxonomy>
 404                   <sequence>
 405                      <domain_architecture length="1279">
 406                         <domain from="5" to="81" confidence="0.59">CARD</domain>
 407                         <domain from="92" to="400" confidence="9.0E-11">NB-ARC</domain>
 408                         <domain from="630" to="668" confidence="1.1E-5">WD40</domain>
 409                      </domain_architecture>
 410                   </sequence>
 411                </clade>
 412             </clade>
 413          </clade>
 414          <clade>
 415             <branch_length>0.18105</branch_length>
 416             <confidence type="unknown">89.0</confidence>
 417             <clade>
 418                <branch_length>0.15891</branch_length>
 419                <confidence type="unknown">64.0</confidence>
 420                <clade>
 421                   <branch_length>0.54836</branch_length>
 422                   <confidence type="unknown">100.0</confidence>
 423                   <clade>
 424                      <branch_length>0.09305</branch_length>
 425                      <confidence type="unknown">46.0</confidence>
 426                      <clade>
 427                         <branch_length>0.21648</branch_length>
 428                         <confidence type="unknown">61.0</confidence>
 429                         <clade>
 430                            <branch_length>0.93134</branch_length>
 431                            <confidence type="unknown">100.0</confidence>
 432                            <clade>
 433                               <name>34_BRAFL</name>
 434                               <branch_length>0.093</branch_length>
 435                               <taxonomy>
 436                                  <code>BRAFL</code>
 437                               </taxonomy>
 438                               <sequence>
 439                                  <domain_architecture length="752">
 440                                     <domain from="49" to="356" confidence="9.0E-6">NB-ARC</domain>
 441                                  </domain_architecture>
 442                               </sequence>
 443                            </clade>
 444                            <clade>
 445                               <name>35_BRAFL</name>
 446                               <branch_length>0.08226</branch_length>
 447                               <taxonomy>
 448                                  <code>BRAFL</code>
 449                               </taxonomy>
 450                               <sequence>
 451                                  <domain_architecture length="753">
 452                                     <domain from="25" to="105" confidence="0.16">DED</domain>
 453                                     <domain from="113" to="409" confidence="1.1E-6">NB-ARC</domain>
 454                                  </domain_architecture>
 455                               </sequence>
 456                            </clade>
 457                         </clade>
 458                         <clade>
 459                            <name>8_BRAFL</name>
 460                            <branch_length>0.58563</branch_length>
 461                            <taxonomy>
 462                               <code>BRAFL</code>
 463                            </taxonomy>
 464                            <sequence>
 465                               <domain_architecture length="916">
 466                                  <domain from="58" to="369" confidence="8.4E-7">NB-ARC</domain>
 467                               </domain_architecture>
 468                            </sequence>
 469                         </clade>
 470                      </clade>
 471                      <clade>
 472                         <branch_length>0.28437</branch_length>
 473                         <confidence type="unknown">84.0</confidence>
 474                         <clade>
 475                            <name>20_NEMVE</name>
 476                            <branch_length>0.71946</branch_length>
 477                            <taxonomy>
 478                               <code>NEMVE</code>
 479                            </taxonomy>
 480                            <sequence>
 481                               <domain_architecture length="786">
 482                                  <domain from="8" to="91" confidence="1.7E-17">DED</domain>
 483                                  <domain from="8" to="85" confidence="0.37">PAAD_DAPIN</domain>
 484                                  <domain from="90" to="388" confidence="6.8E-5">NB-ARC</domain>
 485                                  <domain from="575" to="608" confidence="0.27">TPR_1</domain>
 486                                  <domain from="657" to="690" confidence="0.22">TPR_2</domain>
 487                                  <domain from="698" to="731" confidence="4.2E-5">TPR_2</domain>
 488                               </domain_architecture>
 489                            </sequence>
 490                         </clade>
 491                         <clade>
 492                            <name>21_NEMVE</name>
 493                            <branch_length>0.9571</branch_length>
 494                            <taxonomy>
 495                               <code>NEMVE</code>
 496                            </taxonomy>
 497                            <sequence>
 498                               <domain_architecture length="1563">
 499                                  <domain from="234" to="317" confidence="2.3E-14">CARD</domain>
 500                                  <domain from="238" to="318" confidence="0.5">Death</domain>
 501                                  <domain from="329" to="619" confidence="0.022">NB-ARC</domain>
 502                                  <domain from="906" to="939" confidence="0.17">TPR_1</domain>
 503                                  <domain from="1326" to="1555" confidence="3.2E-26">RVT_1</domain>
 504                               </domain_architecture>
 505                            </sequence>
 506                         </clade>
 507                      </clade>
 508                   </clade>
 509                   <clade>
 510                      <name>9_BRAFL</name>
 511                      <branch_length>1.09612</branch_length>
 512                      <taxonomy>
 513                         <code>BRAFL</code>
 514                      </taxonomy>
 515                      <sequence>
 516                         <domain_architecture length="1011">
 517                            <domain from="5" to="321" confidence="5.0E-5">NB-ARC</domain>
 518                            <domain from="497" to="616" confidence="1.6">BTAD</domain>
 519                            <domain from="500" to="533" confidence="5.6E-4">TPR_1</domain>
 520                            <domain from="542" to="575" confidence="0.43">TPR_1</domain>
 521                            <domain from="626" to="659" confidence="0.0084">TPR_2</domain>
 522                            <domain from="708" to="741" confidence="1.9E-4">TPR_2</domain>
 523                            <domain from="708" to="739" confidence="1.3">TPR_3</domain>
 524                            <domain from="708" to="733" confidence="0.16">TPR_4</domain>
 525                            <domain from="833" to="916" confidence="5.6E-14">Death</domain>
 526                            <domain from="846" to="868" confidence="0.36">LTXXQ</domain>
 527                            <domain from="930" to="1011" confidence="8.3E-17">Death</domain>
 528                         </domain_architecture>
 529                      </sequence>
 530                   </clade>
 531                </clade>
 532                <clade>
 533                   <branch_length>0.34914</branch_length>
 534                   <confidence type="unknown">98.0</confidence>
 535                   <clade>
 536                      <branch_length>0.22189</branch_length>
 537                      <confidence type="unknown">95.0</confidence>
 538                      <clade>
 539                         <name>3_BRAFL</name>
 540                         <branch_length>0.48766</branch_length>
 541                         <taxonomy>
 542                            <code>BRAFL</code>
 543                         </taxonomy>
 544                         <sequence>
 545                            <domain_architecture length="2080">
 546                               <domain from="116" to="423" confidence="1.4E-12">NB-ARC</domain>
 547                               <domain from="620" to="659" confidence="1.4E-6">WD40</domain>
 548                               <domain from="663" to="701" confidence="1.4E-8">WD40</domain>
 549                               <domain from="705" to="743" confidence="3.0E-11">WD40</domain>
 550                               <domain from="747" to="785" confidence="1.1E-8">WD40</domain>
 551                               <domain from="788" to="826" confidence="1.6E-5">WD40</domain>
 552                               <domain from="830" to="870" confidence="1.3E-4">WD40</domain>
 553                               <domain from="874" to="914" confidence="6.2E-9">WD40</domain>
 554                               <domain from="919" to="957" confidence="0.0011">WD40</domain>
 555                               <domain from="961" to="1000" confidence="1.8E-8">WD40</domain>
 556                               <domain from="1013" to="1051" confidence="1.3E-6">WD40</domain>
 557                               <domain from="1055" to="1092" confidence="0.096">WD40</domain>
 558                               <domain from="1794" to="1853" confidence="3.6E-4">Collagen</domain>
 559                            </domain_architecture>
 560                         </sequence>
 561                      </clade>
 562                      <clade>
 563                         <name>2_BRAFL</name>
 564                         <branch_length>0.65293</branch_length>
 565                         <taxonomy>
 566                            <code>BRAFL</code>
 567                         </taxonomy>
 568                         <sequence>
 569                            <domain_architecture length="1691">
 570                               <domain from="162" to="457" confidence="4.4E-10">NB-ARC</domain>
 571                               <domain from="640" to="680" confidence="0.0068">WD40</domain>
 572                               <domain from="684" to="722" confidence="1.6E-8">WD40</domain>
 573                               <domain from="726" to="764" confidence="6.0E-9">WD40</domain>
 574                               <domain from="827" to="865" confidence="6.9E-10">WD40</domain>
 575                               <domain from="868" to="906" confidence="1.2E-6">WD40</domain>
 576                               <domain from="910" to="950" confidence="0.0080">WD40</domain>
 577                               <domain from="954" to="994" confidence="0.0016">WD40</domain>
 578                               <domain from="999" to="1037" confidence="4.9E-6">WD40</domain>
 579                               <domain from="1042" to="1080" confidence="6.3E-8">WD40</domain>
 580                               <domain from="1100" to="1138" confidence="1.9E-8">WD40</domain>
 581                               <domain from="1142" to="1178" confidence="1.4">WD40</domain>
 582                               <domain from="1577" to="1615" confidence="4.3E-4">WD40</domain>
 583                            </domain_architecture>
 584                         </sequence>
 585                      </clade>
 586                   </clade>
 587                   <clade>
 588                      <name>19_NEMVE</name>
 589                      <branch_length>0.57144</branch_length>
 590                      <taxonomy>
 591                         <code>NEMVE</code>
 592                      </taxonomy>
 593                      <sequence>
 594                         <domain_architecture length="1649">
 595                            <domain from="99" to="174" confidence="4.6E-7">DED</domain>
 596                            <domain from="181" to="503" confidence="8.0E-13">NB-ARC</domain>
 597                            <domain from="696" to="734" confidence="1.4E-8">WD40</domain>
 598                            <domain from="738" to="776" confidence="2.9E-9">WD40</domain>
 599                            <domain from="780" to="818" confidence="3.8E-10">WD40</domain>
 600                            <domain from="822" to="860" confidence="6.4E-9">WD40</domain>
 601                            <domain from="864" to="902" confidence="2.1E-10">WD40</domain>
 602                            <domain from="906" to="944" confidence="1.3E-8">WD40</domain>
 603                            <domain from="948" to="986" confidence="1.2E-8">WD40</domain>
 604                            <domain from="990" to="1028" confidence="9.4E-8">WD40</domain>
 605                            <domain from="1032" to="1070" confidence="6.0E-8">WD40</domain>
 606                            <domain from="1074" to="1112" confidence="2.6E-4">WD40</domain>
 607                            <domain from="1364" to="1597" confidence="1.9">SGL</domain>
 608                            <domain from="1442" to="1480" confidence="9.7E-7">WD40</domain>
 609                            <domain from="1527" to="1565" confidence="1.2">WD40</domain>
 610                            <domain from="1568" to="1606" confidence="1.1E-6">WD40</domain>
 611                         </domain_architecture>
 612                      </sequence>
 613                   </clade>
 614                </clade>
 615             </clade>
 616             <clade>
 617                <branch_length>0.43438</branch_length>
 618                <confidence type="unknown">92.0</confidence>
 619                <clade>
 620                   <branch_length>0.92214</branch_length>
 621                   <confidence type="unknown">100.0</confidence>
 622                   <clade>
 623                      <name>37_BRAFL</name>
 624                      <branch_length>0.21133</branch_length>
 625                      <taxonomy>
 626                         <code>BRAFL</code>
 627                      </taxonomy>
 628                      <sequence>
 629                         <domain_architecture length="1793">
 630                            <domain from="6" to="89" confidence="9.6E-13">CARD</domain>
 631                            <domain from="118" to="202" confidence="4.5E-9">CARD</domain>
 632                            <domain from="206" to="491" confidence="0.0011">NB-ARC</domain>
 633                            <domain from="238" to="388" confidence="0.0043">NACHT</domain>
 634                         </domain_architecture>
 635                      </sequence>
 636                   </clade>
 637                   <clade>
 638                      <name>36_BRAFL</name>
 639                      <branch_length>0.16225</branch_length>
 640                      <taxonomy>
 641                         <code>BRAFL</code>
 642                      </taxonomy>
 643                      <sequence>
 644                         <domain_architecture length="918">
 645                            <domain from="9" to="93" confidence="1.6E-9">CARD</domain>
 646                            <domain from="98" to="403" confidence="0.0019">NB-ARC</domain>
 647                         </domain_architecture>
 648                      </sequence>
 649                   </clade>
 650                </clade>
 651                <clade>
 652                   <name>33_BRAFL</name>
 653                   <branch_length>0.8363</branch_length>
 654                   <taxonomy>
 655                      <code>BRAFL</code>
 656                   </taxonomy>
 657                   <sequence>
 658                      <domain_architecture length="1212">
 659                         <domain from="5" to="87" confidence="4.7E-12">Death</domain>
 660                         <domain from="154" to="465" confidence="2.0E-6">NB-ARC</domain>
 661                      </domain_architecture>
 662                   </sequence>
 663                </clade>
 664             </clade>
 665          </clade>
 666       </clade>
 667    </phylogeny>
 668 </phyloxml>