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Suhanaser patch 1 #5

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01f1518
Create non-SRH simulated alignments from PANDIT
suhanaser Feb 7, 2019
7a5d5c8
print directory name while running
suhanaser Feb 7, 2019
0fb27e2
Empirical distribution of GTR parameters
suhanaser Apr 9, 2019
83b3525
New file available
suhanaser Apr 9, 2019
8d92447
extract GTR parameters from IQ-TREE file
suhanaser Apr 16, 2019
0dd2139
gammaproteobacteria dataset Thiergart et. al 2014
suhanaser May 2, 2019
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32,667 changes: 32,667 additions & 0 deletions GTR_param_dist.csv
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30 changes: 30 additions & 0 deletions datasets/Thiergart_2014a/README.yaml
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study:
reference: "Thiergart T, Landan G, Martin WF. 2014. Concatenated alignments and the case of the disappearing tree. BMC Evol. Biol. 14:266."
year: 2014
DOI: dx.doi.org/10.1186/s12862-014-0266-0

dataset:
DOI: dx.doi.org/10.5061/dryad.06640
license: CC0
used for tree inference: yes
alignment:
ntax: 100
nchar: 20920
datatype: protein
partitions: 48
genomes:
mitochondrial: no
nuclear: no
chloroplast: no
dsDNA: no
ssDNA: no
dsRNA: no
ssRNA: no
bacterial: yes
timetree root age: 2480 mya
study root age: NA
study clade:
latin: "Gammaproteobacteria"
english: "Gammaproteobacteria"
taxon ID: 1236
notes: "This is the gammaproteobacteria dataset with 48 genes, figure 1.C in the original paper"
171 changes: 171 additions & 0 deletions datasets/Thiergart_2014a/alignment.nex
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101 changes: 101 additions & 0 deletions datasets/Thiergart_2014a/alignment.nex-seq-summary.txt
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Alignment_name Taxon_name Sequence_length Undetermined_characters Missing_percent A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ?
alignment.nex uid40659 20920 3452 16.501 1699 159 1049 1218 607 1385 354 1021 1040 1546 494 630 694 703 1143 825 905 1380 190 426 0 0 0 0 0 0 3452 0
alignment.nex uid40821 20920 3383 16.171 1691 161 1059 1268 604 1406 341 993 1085 1542 505 635 702 649 1139 775 941 1403 185 453 0 0 0 0 0 0 3383 0
alignment.nex uid41317 20920 3421 16.353 1741 140 1035 1186 630 1433 384 1060 865 1559 483 510 759 706 1258 884 924 1371 175 396 0 0 0 0 0 0 3421 0
alignment.nex uid41333 20920 3478 16.625 1560 154 962 1338 623 1305 352 1084 1175 1559 456 692 691 713 1040 800 917 1390 184 447 0 0 0 0 0 0 3478 0
alignment.nex uid41819 20920 3508 16.769 1745 174 1066 1206 586 1368 346 986 1011 1558 497 594 705 711 1157 798 880 1389 188 447 0 0 0 0 0 0 3508 0
alignment.nex uid42113 20920 3456 16.52 1676 161 1072 1266 598 1396 335 1000 1088 1531 494 643 691 654 1129 775 911 1401 191 452 0 0 0 0 0 0 3456 0
alignment.nex uid42519 20920 3449 16.487 1654 167 1029 1252 603 1401 348 1008 1050 1559 475 637 699 695 1155 805 918 1387 184 445 0 0 0 0 0 0 3449 0
alignment.nex uid43089 20920 3433 16.41 1694 159 1038 1286 594 1400 338 1000 1086 1538 494 631 699 644 1131 774 925 1409 187 460 0 0 0 0 0 0 3433 0
alignment.nex uid43163 20920 3255 15.559 2002 134 1028 1165 571 1490 393 884 901 1652 425 489 776 687 1307 806 913 1434 183 425 0 0 0 0 0 0 3255 0
alignment.nex uid46083 20920 3359 16.056 1794 158 1064 1337 576 1486 368 979 846 1643 437 454 794 638 1404 777 868 1327 183 428 0 0 0 0 0 0 3359 0
alignment.nex uid46099 20920 3670 17.543 1334 191 936 1246 627 1248 435 1164 1165 1623 461 669 660 721 988 942 889 1283 176 492 0 0 0 0 0 0 3670 0
alignment.nex uid46181 20920 3478 16.625 1798 149 1099 1363 581 1463 412 846 803 1574 435 450 809 705 1379 739 844 1420 176 397 0 0 0 0 0 0 3478 0
alignment.nex uid46345 20920 3412 16.31 1558 168 1005 1335 594 1357 362 1082 1105 1558 498 659 668 682 1109 848 946 1326 187 461 0 0 0 0 0 0 3412 0
alignment.nex uid46807 20920 3357 16.047 1680 162 1040 1255 594 1402 341 1015 1065 1556 502 630 696 716 1137 801 934 1393 194 450 0 0 0 0 0 0 3357 0
alignment.nex uid47317 20920 3541 16.926 1636 159 1038 1251 594 1385 354 1010 1061 1542 504 610 690 676 1119 792 921 1403 187 447 0 0 0 0 0 0 3541 0
alignment.nex uid48801 20920 3625 17.328 1319 189 951 1235 623 1246 421 1207 1198 1624 457 684 682 726 965 972 879 1252 177 488 0 0 0 0 0 0 3625 0
alignment.nex uid48809 20920 3143 15.024 1555 151 1163 1135 610 1344 386 1178 1153 1551 503 718 677 748 991 903 1063 1290 172 486 0 0 0 0 0 0 3143 0
alignment.nex uid49133 20920 3443 16.458 1572 163 1004 1327 592 1347 354 1077 1113 1540 501 662 664 678 1098 839 945 1350 188 463 0 0 0 0 0 0 3443 0
alignment.nex uid50119 20920 3350 16.013 1680 137 1013 1266 618 1350 335 1049 1105 1569 450 656 683 801 1055 834 996 1350 169 454 0 0 0 0 0 0 3350 0
alignment.nex uid53371 20920 3494 16.702 1701 151 1060 1334 588 1410 360 993 1072 1545 508 611 688 700 1082 744 898 1393 174 414 0 0 0 0 0 0 3494 0
alignment.nex uid55845 20920 3458 16.53 1689 155 1047 1250 588 1391 340 1014 1051 1549 482 631 689 719 1138 783 925 1381 192 448 0 0 0 0 0 0 3458 0
alignment.nex uid57597 20920 3648 17.438 1729 166 967 1311 594 1460 345 910 950 1656 417 524 729 684 1246 811 783 1368 177 445 0 0 0 0 0 0 3648 0
alignment.nex uid57607 20920 3465 16.563 1669 171 980 1306 617 1472 384 942 857 1623 425 491 780 595 1397 824 825 1473 181 443 0 0 0 0 0 0 3465 0
alignment.nex uid57625 20920 3440 16.444 1619 159 930 1289 641 1231 346 1177 1145 1541 461 719 672 754 1032 826 963 1359 185 431 0 0 0 0 0 0 3440 0
alignment.nex uid57627 20920 3481 16.64 1614 157 969 1343 626 1291 339 1061 1166 1558 453 671 673 713 1034 808 917 1409 186 451 0 0 0 0 0 0 3481 0
alignment.nex uid57631 20920 3478 16.625 1455 153 904 1331 592 1268 379 1134 1199 1678 405 614 738 729 1199 837 889 1274 180 484 0 0 0 0 0 0 3478 0
alignment.nex uid57643 20920 3417 16.334 1642 174 982 1256 639 1278 424 1150 1028 1609 448 618 689 818 1139 825 862 1258 176 488 0 0 0 0 0 0 3417 0
alignment.nex uid57779 20920 3434 16.415 1655 164 1034 1298 599 1393 342 1007 1109 1522 494 637 703 649 1128 779 920 1411 188 454 0 0 0 0 0 0 3434 0
alignment.nex uid57853 20920 3569 17.06 649 239 733 995 808 918 297 2172 2185 1484 367 1366 512 402 717 1203 691 791 169 653 0 0 0 0 0 0 3569 0
alignment.nex uid57855 20920 3390 16.205 1553 168 1073 1335 629 1361 360 1121 1188 1543 498 678 642 622 979 883 990 1333 172 402 0 0 0 0 0 0 3390 0
alignment.nex uid57869 20920 3272 15.641 1650 172 997 1114 585 1373 408 1058 907 1683 448 584 776 675 1277 935 952 1439 187 428 0 0 0 0 0 0 3272 0
alignment.nex uid57921 20920 3518 16.816 1679 168 1043 1298 589 1408 321 996 1124 1509 441 619 683 664 1022 884 922 1413 176 443 0 0 0 0 0 0 3518 0
alignment.nex uid57991 20920 3506 16.759 1644 165 1029 1299 598 1385 337 1001 1107 1519 492 637 698 646 1120 771 917 1410 188 451 0 0 0 0 0 0 3506 0
alignment.nex uid58021 20920 3168 15.143 1616 137 1129 1234 595 1291 361 1128 1068 1551 522 727 706 770 1004 959 1029 1275 173 477 0 0 0 0 0 0 3168 0
alignment.nex uid58087 20920 3473 16.601 1506 146 1084 1396 592 1357 361 938 1160 1536 499 632 695 749 1061 851 897 1368 183 436 0 0 0 0 0 0 3473 0
alignment.nex uid58093 20920 3469 16.582 1602 155 946 1370 634 1295 329 1068 1191 1527 457 722 661 690 1024 806 942 1395 186 451 0 0 0 0 0 0 3469 0
alignment.nex uid58099 20920 3457 16.525 1689 159 1014 1262 603 1443 357 954 1014 1635 462 567 708 693 1149 878 885 1395 176 420 0 0 0 0 0 0 3457 0
alignment.nex uid58111 20920 3529 16.869 1176 197 826 965 611 1115 434 1690 1215 1638 437 920 614 768 998 963 966 1076 190 592 0 0 0 0 0 0 3529 0
alignment.nex uid58169 20920 3373 16.123 1691 158 1109 1343 582 1442 326 880 1031 1600 489 555 740 696 1174 842 877 1425 177 410 0 0 0 0 0 0 3373 0
alignment.nex uid58183 20920 3453 16.506 1483 147 1060 1374 621 1331 381 1021 1209 1508 527 643 684 703 924 898 941 1389 176 447 0 0 0 0 0 0 3453 0
alignment.nex uid58197 20920 3428 16.386 1603 153 984 1357 633 1303 336 1064 1186 1518 469 710 669 685 1046 820 918 1397 184 457 0 0 0 0 0 0 3428 0
alignment.nex uid58213 20920 3457 16.525 1653 166 1033 1298 596 1388 343 1010 1109 1522 494 636 699 644 1122 779 921 1408 188 454 0 0 0 0 0 0 3457 0
alignment.nex uid58247 20920 3446 16.472 1608 153 975 1341 638 1315 337 1078 1181 1513 477 710 672 684 1054 810 919 1377 186 446 0 0 0 0 0 0 3446 0
alignment.nex uid58261 20920 3443 16.458 1653 145 1044 1266 606 1349 356 1041 1094 1568 518 644 672 647 1074 850 949 1407 170 424 0 0 0 0 0 0 3443 0
alignment.nex uid58267 20920 3433 16.41 1660 146 1038 1271 608 1352 357 1027 1095 1571 518 636 676 654 1077 836 955 1410 170 430 0 0 0 0 0 0 3433 0
alignment.nex uid58283 20920 3537 16.907 1561 148 1046 1321 637 1334 349 1023 1135 1496 479 669 673 707 1008 902 912 1385 184 414 0 0 0 0 0 0 3537 0
alignment.nex uid58393 20920 3457 16.525 1653 164 1034 1295 598 1392 341 1007 1110 1520 494 638 701 646 1125 772 922 1410 188 453 0 0 0 0 0 0 3457 0
alignment.nex uid58403 20920 3484 16.654 1550 161 874 1342 585 1393 402 1074 927 1676 417 509 789 764 1315 848 856 1308 186 460 0 0 0 0 0 0 3484 0
alignment.nex uid58431 20920 3535 16.898 1580 137 1064 1298 619 1340 342 1081 1168 1514 480 692 663 659 999 843 952 1358 171 425 0 0 0 0 0 0 3535 0
alignment.nex uid58459 20920 3131 14.967 1624 132 1127 1264 594 1337 362 1103 1112 1544 511 691 701 807 1002 939 979 1312 172 476 0 0 0 0 0 0 3131 0
alignment.nex uid58467 20920 3444 16.463 1775 146 1088 1394 555 1531 413 780 767 1591 420 426 814 717 1475 678 814 1462 190 440 0 0 0 0 0 0 3444 0
alignment.nex uid58473 20920 3479 16.63 1785 150 1060 1453 547 1524 416 785 651 1560 393 412 814 701 1545 760 843 1415 186 441 0 0 0 0 0 0 3479 0
alignment.nex uid58483 20920 3468 16.577 1544 150 1015 1362 605 1378 344 992 1173 1543 480 597 716 687 1078 891 837 1446 171 443 0 0 0 0 0 0 3468 0
alignment.nex uid58499 20920 3594 17.18 1333 175 1058 1239 658 1181 340 1281 1483 1492 444 828 604 624 813 994 863 1250 155 511 0 0 0 0 0 0 3594 0
alignment.nex uid58521 20920 3408 16.291 1586 179 1011 1282 641 1339 351 1128 1200 1575 461 674 646 678 974 889 950 1343 171 434 0 0 0 0 0 0 3408 0
alignment.nex uid58553 20920 3457 16.525 1711 171 1037 1194 599 1390 378 987 976 1570 493 575 703 713 1191 810 914 1412 186 453 0 0 0 0 0 0 3457 0
alignment.nex uid58613 20920 3511 16.783 1817 154 982 1191 593 1480 435 954 701 1702 430 448 850 697 1424 783 813 1356 184 415 0 0 0 0 0 0 3511 0
alignment.nex uid58617 20920 3353 16.028 1781 169 1012 1320 586 1404 374 1038 1107 1541 534 615 683 643 1101 777 880 1391 177 434 0 0 0 0 0 0 3353 0
alignment.nex uid58639 20920 3466 16.568 1734 154 1019 1277 596 1437 349 965 1027 1617 447 575 716 713 1158 817 879 1364 178 432 0 0 0 0 0 0 3466 0
alignment.nex uid58715 20920 3462 16.549 1631 149 1040 1309 611 1347 349 986 1078 1541 487 619 651 702 1047 941 901 1461 173 435 0 0 0 0 0 0 3462 0
alignment.nex uid58725 20920 3430 16.396 1639 172 1049 1253 609 1402 348 985 1074 1559 501 614 691 702 1135 807 927 1399 186 438 0 0 0 0 0 0 3430 0
alignment.nex uid58765 20920 3503 16.745 1660 135 999 1261 613 1348 339 1052 1094 1549 445 661 681 794 1038 827 962 1337 169 453 0 0 0 0 0 0 3503 0
alignment.nex uid58789 20920 3490 16.683 1592 155 962 1362 639 1291 328 1071 1174 1495 468 708 673 674 1045 835 929 1421 184 424 0 0 0 0 0 0 3490 0
alignment.nex uid58811 20920 3592 17.17 1324 177 1052 1241 658 1179 342 1293 1488 1497 443 833 600 620 812 995 861 1248 155 510 0 0 0 0 0 0 3592 0
alignment.nex uid58907 20920 3457 16.525 1631 164 1010 1465 632 1378 338 1027 1153 1471 514 681 641 631 1024 785 949 1373 176 420 0 0 0 0 0 0 3457 0
alignment.nex uid58915 20920 3434 16.415 1665 161 1053 1276 604 1399 339 1030 1094 1504 498 643 696 654 1129 763 939 1396 188 455 0 0 0 0 0 0 3434 0
alignment.nex uid59131 20920 3380 16.157 1915 133 1074 1174 577 1479 375 890 918 1616 416 488 758 655 1276 811 919 1456 189 421 0 0 0 0 0 0 3380 0
alignment.nex uid59139 20920 3338 15.956 1707 153 1006 1220 578 1422 362 1018 1067 1607 436 610 697 717 1086 875 916 1458 183 464 0 0 0 0 0 0 3338 0
alignment.nex uid59151 20920 3449 16.487 1645 161 1042 1255 599 1389 359 1021 1065 1548 507 611 692 682 1126 801 924 1408 188 448 0 0 0 0 0 0 3449 0
alignment.nex uid59179 20920 3524 16.845 1753 140 1012 1336 582 1488 402 883 907 1612 483 465 780 651 1327 774 818 1388 178 417 0 0 0 0 0 0 3524 0
alignment.nex uid59209 20920 3472 16.597 1452 144 1096 1386 609 1359 358 1066 1225 1475 486 631 702 703 1003 870 882 1367 177 457 0 0 0 0 0 0 3472 0
alignment.nex uid59243 20920 3402 16.262 1535 171 1014 1316 586 1358 357 1113 1133 1548 504 666 685 661 1113 852 914 1351 182 459 0 0 0 0 0 0 3402 0
alignment.nex uid59251 20920 3451 16.496 1611 169 1028 1420 648 1374 346 1066 1142 1475 509 663 635 621 1023 822 966 1362 176 413 0 0 0 0 0 0 3451 0
alignment.nex uid59267 20920 3511 16.783 1662 162 1044 1327 600 1375 325 956 1066 1548 451 596 692 683 1063 912 921 1404 176 446 0 0 0 0 0 0 3511 0
alignment.nex uid59289 20920 3524 16.845 1316 193 927 1214 643 1197 436 1265 1217 1631 466 647 690 760 1055 985 921 1166 194 473 0 0 0 0 0 0 3524 0
alignment.nex uid59295 20920 3467 16.573 1642 158 1072 1245 586 1370 351 1044 1070 1544 490 630 696 682 1131 822 922 1377 181 440 0 0 0 0 0 0 3467 0
alignment.nex uid59297 20920 3450 16.491 1662 166 1041 1243 602 1394 347 1000 1047 1559 475 635 694 702 1151 802 929 1390 185 446 0 0 0 0 0 0 3450 0
alignment.nex uid59395 20920 3431 16.401 1735 177 994 1267 595 1355 372 1019 1087 1587 504 598 685 705 1084 797 951 1374 176 427 0 0 0 0 0 0 3431 0
alignment.nex uid59407 20920 3449 16.487 1575 160 972 1344 633 1308 353 1065 1176 1540 462 698 679 716 1049 796 909 1404 184 448 0 0 0 0 0 0 3449 0
alignment.nex uid59419 20920 3486 16.663 1587 139 1058 1377 573 1450 361 918 1058 1505 483 610 731 684 1166 779 877 1440 175 463 0 0 0 0 0 0 3486 0
alignment.nex uid59431 20920 3434 16.415 1667 161 1053 1276 604 1401 338 1030 1094 1504 497 640 698 655 1130 761 937 1397 188 455 0 0 0 0 0 0 3434 0
alignment.nex uid59969 20920 3456 16.52 1699 161 1070 1264 599 1408 345 1005 1081 1528 492 625 692 644 1126 775 913 1398 187 452 0 0 0 0 0 0 3456 0
alignment.nex uid61593 20920 3467 16.573 1542 170 1004 1322 583 1350 361 1110 1109 1538 496 657 684 674 1110 828 930 1348 182 455 0 0 0 0 0 0 3467 0
alignment.nex uid61599 20920 3436 16.424 1562 165 1023 1339 602 1340 358 1108 1107 1537 490 668 690 660 1110 804 949 1333 186 453 0 0 0 0 0 0 3436 0
alignment.nex uid62105 20920 3267 15.617 2003 118 1021 1277 572 1540 354 880 931 1607 402 465 790 643 1340 773 857 1466 190 424 0 0 0 0 0 0 3267 0
alignment.nex uid62715 20920 3421 16.353 1614 162 1066 1271 609 1394 343 1014 1085 1547 497 624 700 671 1111 826 948 1395 185 437 0 0 0 0 0 0 3421 0
alignment.nex uid62921 20920 3489 16.678 1754 143 1151 1296 584 1423 375 843 901 1571 464 518 745 665 1249 810 901 1426 185 427 0 0 0 0 0 0 3489 0
alignment.nex uid62923 20920 3691 17.643 1605 162 1036 1349 625 1360 334 1038 1140 1481 510 662 650 607 1015 787 932 1358 174 404 0 0 0 0 0 0 3691 0
alignment.nex uid64753 20920 3491 16.687 1591 146 1065 1322 602 1349 331 984 1103 1517 467 638 655 713 1030 961 897 1439 172 447 0 0 0 0 0 0 3491 0
alignment.nex uid66323 20920 3568 17.055 1753 170 1009 1306 586 1386 365 1018 1101 1528 532 617 666 638 1077 749 880 1364 175 432 0 0 0 0 0 0 3568 0
alignment.nex uid66567 20920 3476 16.616 1566 161 969 1344 595 1282 348 1103 1172 1570 467 701 681 756 1037 778 890 1360 182 482 0 0 0 0 0 0 3476 0
alignment.nex uid67313 20920 3447 16.477 1649 172 1039 1267 610 1399 351 987 1074 1555 494 616 691 698 1128 796 916 1407 186 438 0 0 0 0 0 0 3447 0
alignment.nex uid67349 20920 3560 17.017 1551 153 1052 1377 605 1339 345 1016 1145 1508 470 676 680 628 1007 869 951 1370 181 437 0 0 0 0 0 0 3560 0
alignment.nex uid67363 20920 3493 16.697 1576 177 1008 1240 630 1338 381 1111 1109 1560 480 637 684 741 1013 930 837 1346 176 453 0 0 0 0 0 0 3493 0
alignment.nex uid67387 20920 3511 16.783 1841 161 979 1169 588 1453 460 963 719 1732 433 454 824 725 1381 802 804 1331 185 405 0 0 0 0 0 0 3511 0
alignment.nex uid67391 20920 3511 16.783 1630 158 1013 1211 614 1319 381 1004 1061 1598 516 612 700 842 1007 843 905 1368 171 456 0 0 0 0 0 0 3511 0
alignment.nex uid68057 20920 3519 16.821 1673 168 973 1384 619 1364 357 1027 1140 1469 531 663 658 642 1029 790 937 1377 174 426 0 0 0 0 0 0 3519 0
alignment.nex uid68739 20920 3570 17.065 1405 215 895 1067 599 1243 429 1250 1033 1590 506 752 640 751 1107 884 976 1315 183 510 0 0 0 0 0 0 3570 0
alignment.nex uid72473 20920 3290 15.727 1978 118 1055 1207 584 1499 351 893 936 1602 418 506 750 691 1266 819 907 1447 188 415 0 0 0 0 0 0 3290 0
alignment.nex uid73759 20920 3541 16.926 1541 154 1025 1330 607 1334 345 1073 1208 1493 487 656 677 658 955 914 944 1365 181 432 0 0 0 0 0 0 3541 0
2 changes: 2 additions & 0 deletions datasets/Thiergart_2014a/alignment.nex-summary.txt
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Alignment_name No_of_taxa Alignment_length Total_matrix_cells Undetermined_characters Missing_percent No_variable_sites Proportion_variable_sites Parsimony_informative_sites Proportion_parsimony_informative A C D E F G H I K L M N P Q R S T V W Y B J Z X . * - ?
alignment.nex 100 20920 2092000 345576 16.519 15697 0.75 13614 0.651 162449 15984 102119 128312 60644 136475 36154 104701 108675 155917 47439 63198 69784 68863 111240 83747 91034 136794 18071 44824 0 0 0 0 0 0 345576 0
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