Lines Matching refs:cnt
751 int cnt; in parseArg() local
1143 for (cnt = 1; cnt < argc; cnt++) { in parseArg()
1146 if (strcmp(argv[cnt], "-h") == 0 || strcmp(argv[cnt], "--help") == 0) { in parseArg()
1148 usage_iqtree(argv, strcmp(argv[cnt], "--help") == 0); in parseArg()
1154 …if (strcmp(argv[cnt], "-V") == 0 || strcmp(argv[cnt], "-version") == 0 || strcmp(argv[cnt], "--ver… in parseArg()
1158 if (strcmp(argv[cnt], "-ho") == 0 || strcmp(argv[cnt], "-?") == 0) { in parseArg()
1162 if (strcmp(argv[cnt], "-hh") == 0 || strcmp(argv[cnt], "-hhh") == 0) { in parseArg()
1170 if (strcmp(argv[cnt], "-v0") == 0) { in parseArg()
1174 if (strcmp(argv[cnt], "-v") == 0 || strcmp(argv[cnt], "--verbose") == 0) { in parseArg()
1178 if (strcmp(argv[cnt], "-vv") == 0 in parseArg()
1179 || strcmp(argv[cnt], "-v2") == 0) { in parseArg()
1183 if (strcmp(argv[cnt], "-vvv") == 0 in parseArg()
1184 || strcmp(argv[cnt], "-v3") == 0) { in parseArg()
1188 if (strcmp(argv[cnt], "-k") == 0) { in parseArg()
1189 cnt++; in parseArg()
1190 if (cnt >= argc) in parseArg()
1192 convert_range(argv[cnt], params.min_size, params.sub_size, in parseArg()
1197 if (strcmp(argv[cnt], "-pre") == 0 || strcmp(argv[cnt], "--prefix") == 0) { in parseArg()
1198 cnt++; in parseArg()
1199 if (cnt >= argc) in parseArg()
1201 params.out_prefix = argv[cnt]; in parseArg()
1204 if (strcmp(argv[cnt], "-pp") == 0) { in parseArg()
1205 cnt++; in parseArg()
1206 if (cnt >= argc) in parseArg()
1208 convert_range(argv[cnt], params.min_proportion, in parseArg()
1214 if (strcmp(argv[cnt], "-mk") == 0) { in parseArg()
1215 cnt++; in parseArg()
1216 if (cnt >= argc) in parseArg()
1218 params.min_size = convert_int(argv[cnt]); in parseArg()
1221 if (strcmp(argv[cnt], "-bud") == 0) { in parseArg()
1222 cnt++; in parseArg()
1223 if (cnt >= argc) in parseArg()
1225 convert_range(argv[cnt], params.min_budget, params.budget, in parseArg()
1229 if (strcmp(argv[cnt], "-mb") == 0) { in parseArg()
1230 cnt++; in parseArg()
1231 if (cnt >= argc) in parseArg()
1233 params.min_budget = convert_int(argv[cnt]); in parseArg()
1236 if (strcmp(argv[cnt], "-o") == 0) { in parseArg()
1237 cnt++; in parseArg()
1238 if (cnt >= argc) in parseArg()
1240 params.root = argv[cnt]; in parseArg()
1243 if (strcmp(argv[cnt], "-optalg") == 0) { in parseArg()
1244 cnt++; in parseArg()
1245 if (cnt >= argc) in parseArg()
1247 params.optimize_alg = argv[cnt]; in parseArg()
1250 if (strcmp(argv[cnt], "-optlen") == 0) { in parseArg()
1251 cnt++; in parseArg()
1252 if (cnt >= argc) in parseArg()
1254 params.optimize_alg_mixlen = argv[cnt]; in parseArg()
1257 if (strcmp(argv[cnt], "-optalg_gammai") == 0) { in parseArg()
1258 cnt++; in parseArg()
1259 if (cnt >= argc) in parseArg()
1261 params.optimize_alg_gammai = argv[cnt]; in parseArg()
1264 if (strcmp(argv[cnt], "-root") == 0 || strcmp(argv[cnt], "-rooted") == 0) { in parseArg()
1269 if (strcmp(argv[cnt], "--root-dist") == 0) { in parseArg()
1270 cnt++; in parseArg()
1271 if (cnt >= argc) in parseArg()
1273 params.root_move_dist = convert_int(argv[cnt]); in parseArg()
1277 if (strcmp(argv[cnt], "--root-find") == 0) { in parseArg()
1282 if (strcmp(argv[cnt], "--root-test") == 0) { in parseArg()
1287 if (strcmp(argv[cnt], "-all") == 0) { in parseArg()
1291 if (strcmp(argv[cnt], "--greedy") == 0) { in parseArg()
1295 if (strcmp(argv[cnt], "-pr") == 0 in parseArg()
1296 || strcmp(argv[cnt], "--pruning") == 0) { in parseArg()
1302 if (strcmp(argv[cnt], "-e") == 0) { in parseArg()
1303 cnt++; in parseArg()
1304 if (cnt >= argc) in parseArg()
1306 params.param_file = argv[cnt]; in parseArg()
1309 if (strcmp(argv[cnt], "-if") == 0) { in parseArg()
1310 cnt++; in parseArg()
1311 if (cnt >= argc) in parseArg()
1313 params.initial_file = argv[cnt]; in parseArg()
1316 if (strcmp(argv[cnt], "-nni_nr_step") == 0) { in parseArg()
1317 cnt++; in parseArg()
1318 if (cnt >= argc) in parseArg()
1320 NNI_MAX_NR_STEP = convert_int(argv[cnt]); in parseArg()
1323 if (strcmp(argv[cnt], "-ia") == 0) { in parseArg()
1324 cnt++; in parseArg()
1325 if (cnt >= argc) in parseArg()
1327 params.initial_area_file = argv[cnt]; in parseArg()
1330 if (strcmp(argv[cnt], "-u") == 0) { in parseArg()
1332 cnt++; in parseArg()
1333 if (cnt >= argc) in parseArg()
1335 params.budget_file = argv[cnt]; in parseArg()
1338 if (strcmp(argv[cnt], "-dd") == 0) { in parseArg()
1340 cnt++; in parseArg()
1341 if (cnt >= argc) in parseArg()
1344 params.sample_size = convert_int(argv[cnt]); in parseArg()
1347 if (strcmp(argv[cnt], "-ts") == 0) { in parseArg()
1349 cnt++; in parseArg()
1351 if (cnt >= argc) in parseArg()
1353 params.pdtaxa_file = argv[cnt]; in parseArg()
1356 if (strcmp(argv[cnt], "-bound") == 0) { in parseArg()
1358 cnt++; in parseArg()
1359 if (cnt >= argc) in parseArg()
1361 params.areas_boundary_file = argv[cnt]; in parseArg()
1364 if (strcmp(argv[cnt], "-blm") == 0) { in parseArg()
1366 cnt++; in parseArg()
1367 if (cnt >= argc) in parseArg()
1369 params.boundary_modifier = convert_double(argv[cnt]); in parseArg()
1372 if (strcmp(argv[cnt], "-dist") == 0 in parseArg()
1373 || strcmp(argv[cnt], "-d") == 0) { in parseArg()
1376 cnt++; in parseArg()
1377 if (cnt >= argc) in parseArg()
1379 params.dist_file = argv[cnt]; in parseArg()
1382 if (strcmp(argv[cnt], "-djc") == 0) { in parseArg()
1386 if (strcmp(argv[cnt], "-dobs") == 0) { in parseArg()
1390 if (strcmp(argv[cnt], "-r") == 0) { in parseArg()
1391 cnt++; in parseArg()
1392 if (cnt >= argc) in parseArg()
1394 params.sub_size = convert_int(argv[cnt]); in parseArg()
1398 if (strcmp(argv[cnt], "-rs") == 0) { in parseArg()
1399 cnt++; in parseArg()
1400 if (cnt >= argc) in parseArg()
1403 params.aln_file = argv[cnt]; in parseArg()
1406 if (strcmp(argv[cnt], "-rstar") == 0) { in parseArg()
1407 cnt++; in parseArg()
1408 if (cnt >= argc) in parseArg()
1410 params.sub_size = convert_int(argv[cnt]); in parseArg()
1414 if (strcmp(argv[cnt], "-ru") == 0) { in parseArg()
1415 cnt++; in parseArg()
1416 if (cnt >= argc) in parseArg()
1418 params.sub_size = convert_int(argv[cnt]); in parseArg()
1422 if (strcmp(argv[cnt], "-rcat") == 0) { in parseArg()
1423 cnt++; in parseArg()
1424 if (cnt >= argc) in parseArg()
1426 params.sub_size = convert_int(argv[cnt]); in parseArg()
1430 if (strcmp(argv[cnt], "-rbal") == 0) { in parseArg()
1431 cnt++; in parseArg()
1432 if (cnt >= argc) in parseArg()
1434 params.sub_size = convert_int(argv[cnt]); in parseArg()
1438 if (strcmp(argv[cnt], "--rand") == 0) { in parseArg()
1439 cnt++; in parseArg()
1440 if (cnt >= argc) in parseArg()
1442 if (strcmp(argv[cnt], "UNI") == 0) in parseArg()
1444 else if (strcmp(argv[cnt], "CAT") == 0) in parseArg()
1446 else if (strcmp(argv[cnt], "BAL") == 0) in parseArg()
1448 else if (strcmp(argv[cnt], "NET") == 0) in parseArg()
1455 if (strcmp(argv[cnt], "--keep-ident") == 0 || strcmp(argv[cnt], "-keep-ident") == 0) { in parseArg()
1459 if (strcmp(argv[cnt], "-rcsg") == 0) { in parseArg()
1460 cnt++; in parseArg()
1461 if (cnt >= argc) in parseArg()
1463 params.sub_size = convert_int(argv[cnt]); in parseArg()
1467 if (strcmp(argv[cnt], "-rpam") == 0) { in parseArg()
1468 cnt++; in parseArg()
1469 if (cnt >= argc) in parseArg()
1471 params.num_splits = convert_int(argv[cnt]); in parseArg()
1474 if (strcmp(argv[cnt], "-rlen") == 0 || strcmp(argv[cnt], "--rlen") == 0) { in parseArg()
1475 cnt++; in parseArg()
1476 if (cnt >= argc - 2) in parseArg()
1478 params.min_len = convert_double(argv[cnt]); in parseArg()
1479 params.mean_len = convert_double(argv[cnt + 1]); in parseArg()
1480 params.max_len = convert_double(argv[cnt + 2]); in parseArg()
1481 cnt += 2; in parseArg()
1484 if (strcmp(argv[cnt], "-rzero") == 0) { in parseArg()
1485 cnt++; in parseArg()
1486 if (cnt >= argc) in parseArg()
1488 params.num_zero_len = convert_int(argv[cnt]); in parseArg()
1493 if (strcmp(argv[cnt], "-rset") == 0) { in parseArg()
1494 cnt++; in parseArg()
1495 if (cnt >= argc - 1) in parseArg()
1497 params.overlap = convert_int(argv[cnt]); in parseArg()
1498 cnt++; in parseArg()
1499 params.pdtaxa_file = argv[cnt]; in parseArg()
1503 if (strcmp(argv[cnt], "-rep") == 0) { in parseArg()
1504 cnt++; in parseArg()
1505 if (cnt >= argc) in parseArg()
1507 params.repeated_time = convert_int(argv[cnt]); in parseArg()
1510 if (strcmp(argv[cnt], "-lim") == 0) { in parseArg()
1511 cnt++; in parseArg()
1512 if (cnt >= argc) in parseArg()
1514 params.pd_limit = convert_int(argv[cnt]); in parseArg()
1517 if (strcmp(argv[cnt], "-noout") == 0) { in parseArg()
1521 if (strcmp(argv[cnt], "-1out") == 0) { in parseArg()
1525 if (strcmp(argv[cnt], "-oldout") == 0) { in parseArg()
1529 if (strcmp(argv[cnt], "-nexout") == 0) { in parseArg()
1533 if (strcmp(argv[cnt], "-exhaust") == 0) { in parseArg()
1537 if (strcmp(argv[cnt], "-seed") == 0 || strcmp(argv[cnt], "--seed") == 0) { in parseArg()
1538 cnt++; in parseArg()
1539 if (cnt >= argc) in parseArg()
1541 params.ran_seed = abs(convert_int(argv[cnt])); in parseArg()
1544 if (strcmp(argv[cnt], "-pdgain") == 0) { in parseArg()
1548 if (strcmp(argv[cnt], "-sup") == 0 || strcmp(argv[cnt], "--support") == 0) { in parseArg()
1549 cnt++; in parseArg()
1550 if (cnt >= argc) in parseArg()
1552 params.second_tree = argv[cnt]; in parseArg()
1556 if (strcmp(argv[cnt], "-suptag") == 0 || strcmp(argv[cnt], "--suptag") == 0) { in parseArg()
1557 cnt++; in parseArg()
1558 if (cnt >= argc) in parseArg()
1560 params.support_tag = argv[cnt]; in parseArg()
1563 if (strcmp(argv[cnt], "-sup2") == 0) { in parseArg()
1567 if (strcmp(argv[cnt], "--gcf") == 0) { in parseArg()
1569 cnt++; in parseArg()
1570 if (cnt >= argc) in parseArg()
1572 params.treeset_file = argv[cnt]; in parseArg()
1575 if (strcmp(argv[cnt], "--scf") == 0) { in parseArg()
1577 cnt++; in parseArg()
1578 if (cnt >= argc) in parseArg()
1580 params.site_concordance = convert_int(argv[cnt]); in parseArg()
1585 if (strcmp(argv[cnt], "--scf-part") == 0 || strcmp(argv[cnt], "--cf-verbose") == 0) { in parseArg()
1589 if (strcmp(argv[cnt], "--df-tree") == 0) { in parseArg()
1593 if (strcmp(argv[cnt], "--qic") == 0) { in parseArg()
1597 if (strcmp(argv[cnt], "-treew") == 0) { in parseArg()
1598 cnt++; in parseArg()
1599 if (cnt >= argc) in parseArg()
1601 params.tree_weight_file = argv[cnt]; in parseArg()
1604 if (strcmp(argv[cnt], "-con") == 0 || strcmp(argv[cnt], "--contree") == 0) { in parseArg()
1608 if (strcmp(argv[cnt], "-net") == 0 || strcmp(argv[cnt], "--connet") == 0) { in parseArg()
1614 if (strcmp(argv[cnt], "-comp") == 0) { in parseArg()
1615 cnt++; in parseArg()
1616 if (cnt >= argc) in parseArg()
1619 params.second_tree = argv[cnt]; in parseArg()
1622 if (strcmp(argv[cnt], "-stats") == 0) { in parseArg()
1626 if (strcmp(argv[cnt], "-gbo") == 0) { //guided bootstrap in parseArg()
1627 cnt++; in parseArg()
1628 if (cnt >= argc) in parseArg()
1630 params.siteLL_file = argv[cnt]; in parseArg()
1635 if (strcmp(argv[cnt], "-mprob") == 0) { //compute multinomial distribution probability in parseArg()
1636 cnt++; in parseArg()
1637 if (cnt >= argc) in parseArg()
1639 params.second_align = argv[cnt]; in parseArg()
1644 if (strcmp(argv[cnt], "-min") == 0) { in parseArg()
1648 if (strcmp(argv[cnt], "-excl") == 0) { in parseArg()
1652 if (strcmp(argv[cnt], "-endem") == 0) { in parseArg()
1656 if (strcmp(argv[cnt], "-compl") == 0) { in parseArg()
1657 cnt++; in parseArg()
1658 if (cnt >= argc) in parseArg()
1660 params.complement_area = argv[cnt]; in parseArg()
1663 if (strcmp(argv[cnt], "-cluster") == 0) { in parseArg()
1665 cnt++; in parseArg()
1666 if (cnt >= argc) in parseArg()
1668 params.taxa_order_file = argv[cnt]; in parseArg()
1671 if (strcmp(argv[cnt], "-taxa") == 0) { in parseArg()
1675 if (strcmp(argv[cnt], "-area") == 0) { in parseArg()
1679 if (strcmp(argv[cnt], "-scale") == 0) { in parseArg()
1680 cnt++; in parseArg()
1681 if (cnt >= argc) in parseArg()
1683 params.scaling_factor = convert_double(argv[cnt]); in parseArg()
1686 if (strcmp(argv[cnt], "-scaleg") == 0) { in parseArg()
1687 cnt++; in parseArg()
1688 if (cnt >= argc) in parseArg()
1690 params.gene_scale_factor = convert_double(argv[cnt]); in parseArg()
1693 if (strcmp(argv[cnt], "-scalebranch") == 0) { in parseArg()
1695 cnt++; in parseArg()
1696 if (cnt >= argc) in parseArg()
1698 params.scaling_factor = convert_double(argv[cnt]); in parseArg()
1701 if (strcmp(argv[cnt], "-scalenode") == 0) { in parseArg()
1703 cnt++; in parseArg()
1704 if (cnt >= argc) in parseArg()
1706 params.scaling_factor = convert_double(argv[cnt]); in parseArg()
1709 if (strcmp(argv[cnt], "-prec") == 0) { in parseArg()
1710 cnt++; in parseArg()
1711 if (cnt >= argc) in parseArg()
1713 params.numeric_precision = convert_int(argv[cnt]); in parseArg()
1716 if (strcmp(argv[cnt], "-lp") == 0) { in parseArg()
1720 if (strcmp(argv[cnt], "-lpbin") == 0) { in parseArg()
1725 if (strcmp(argv[cnt], "-qp") == 0) { in parseArg()
1730 if (strcmp(argv[cnt], "-quiet") == 0 || strcmp(argv[cnt], "--quiet") == 0) { in parseArg()
1734 if (strcmp(argv[cnt], "-mult") == 0) { in parseArg()
1738 if (strcmp(argv[cnt], "-bi") == 0 || strcmp(argv[cnt], "--burnin") == 0) { in parseArg()
1739 cnt++; in parseArg()
1740 if (cnt >= argc) in parseArg()
1742 params.tree_burnin = convert_int(argv[cnt]); in parseArg()
1747 if (strcmp(argv[cnt], "-tm") == 0) { in parseArg()
1748 cnt++; in parseArg()
1749 if (cnt >= argc) in parseArg()
1751 params.tree_max_count = convert_int(argv[cnt]); in parseArg()
1756 if (strcmp(argv[cnt], "-minsup") == 0 || strcmp(argv[cnt], "--sup-min") == 0) { in parseArg()
1757 cnt++; in parseArg()
1758 if (cnt >= argc) in parseArg()
1760 params.split_threshold = convert_double(argv[cnt]); in parseArg()
1765 if (strcmp(argv[cnt], "-minsupnew") == 0) { in parseArg()
1766 cnt++; in parseArg()
1767 if (cnt >= argc) in parseArg()
1769 params.split_threshold_str = argv[cnt]; in parseArg()
1772 if (strcmp(argv[cnt], "-tw") == 0) { in parseArg()
1773 cnt++; in parseArg()
1774 if (cnt >= argc) in parseArg()
1776 params.split_weight_threshold = convert_double(argv[cnt]); in parseArg()
1782 if (strcmp(argv[cnt], "-czb") == 0 || strcmp(argv[cnt], "--polytomy") == 0) { in parseArg()
1787 if (strcmp(argv[cnt], "-swc") == 0) { in parseArg()
1791 if (strcmp(argv[cnt], "-swa") == 0) { in parseArg()
1795 if (strcmp(argv[cnt], "-swp") == 0) { in parseArg()
1799 if (strcmp(argv[cnt], "-iwc") == 0) { in parseArg()
1803 …if (strcmp(argv[cnt], "--aln") == 0 || strcmp(argv[cnt], "--msa") == 0 || strcmp(argv[cnt], "-s") … in parseArg()
1804 cnt++; in parseArg()
1805 if (cnt >= argc) in parseArg()
1807 params.aln_file = argv[cnt]; in parseArg()
1810 if (strcmp(argv[cnt], "--sequential") == 0) { in parseArg()
1814 if (strcmp(argv[cnt], "--symtest") == 0) { in parseArg()
1819 if (strcmp(argv[cnt], "--bisymtest") == 0) { in parseArg()
1824 if (strcmp(argv[cnt], "--symtest-only") == 0) { in parseArg()
1831 if (strcmp(argv[cnt], "--symtest-remove-bad") == 0) { in parseArg()
1838 if (strcmp(argv[cnt], "--symtest-remove-good") == 0) { in parseArg()
1845 if (strcmp(argv[cnt], "--symtest-keep-zero") == 0) { in parseArg()
1850 if (strcmp(argv[cnt], "--symtest-type") == 0) { in parseArg()
1851 cnt++; in parseArg()
1852 if (cnt >= argc) in parseArg()
1854 if (strcmp(argv[cnt], "SYM") == 0) in parseArg()
1856 else if (strcmp(argv[cnt], "MAR") == 0) in parseArg()
1858 else if (strcmp(argv[cnt], "INT") == 0) in parseArg()
1867 if (strcmp(argv[cnt], "--symtest-pval") == 0) { in parseArg()
1868 cnt++; in parseArg()
1869 if (cnt >= argc) in parseArg()
1871 params.symtest_pcutoff = convert_double(argv[cnt]); in parseArg()
1879 if (strcmp(argv[cnt], "--symstat") == 0) { in parseArg()
1886 if (strcmp(argv[cnt], "--symtest-perm") == 0) { in parseArg()
1887 cnt++; in parseArg()
1888 if (cnt >= argc) in parseArg()
1890 params.symtest_shuffle = convert_int(argv[cnt]); in parseArg()
1898 if (strcmp(argv[cnt], "-z") == 0 || strcmp(argv[cnt], "--trees") == 0) { in parseArg()
1899 cnt++; in parseArg()
1900 if (cnt >= argc) in parseArg()
1902 params.treeset_file = argv[cnt]; in parseArg()
1905 if (strcmp(argv[cnt], "-zb") == 0 || strcmp(argv[cnt], "--test") == 0) { in parseArg()
1906 cnt++; in parseArg()
1907 if (cnt >= argc) in parseArg()
1909 params.topotest_replicates = convert_int(argv[cnt]); in parseArg()
1914 if (strcmp(argv[cnt], "--estimate-model") == 0) { in parseArg()
1918 if (strcmp(argv[cnt], "-zw") == 0 || strcmp(argv[cnt], "--test-weight") == 0) { in parseArg()
1922 if (strcmp(argv[cnt], "-au") == 0 || strcmp(argv[cnt], "--test-au") == 0) { in parseArg()
1926 if (strcmp(argv[cnt], "-sp") == 0 || strcmp(argv[cnt], "-Q") == 0) { in parseArg()
1927 cnt++; in parseArg()
1928 if (cnt >= argc) in parseArg()
1930 params.partition_file = argv[cnt]; in parseArg()
1933 …if (strcmp(argv[cnt], "-spp") == 0 || strcmp(argv[cnt], "-p") == 0 || strcmp(argv[cnt], "--partiti… in parseArg()
1934 cnt++; in parseArg()
1935 if (cnt >= argc) in parseArg()
1937 params.partition_file = argv[cnt]; in parseArg()
1942 if (strcmp(argv[cnt], "-spj") == 0 || strcmp(argv[cnt], "-q") == 0) { in parseArg()
1943 cnt++; in parseArg()
1944 if (cnt >= argc) in parseArg()
1946 params.partition_file = argv[cnt]; in parseArg()
1952 if (strcmp(argv[cnt], "-M") == 0) { in parseArg()
1957 if (strcmp(argv[cnt], "-spu") == 0 || strcmp(argv[cnt], "-S") == 0) { in parseArg()
1958 cnt++; in parseArg()
1959 if (cnt >= argc) in parseArg()
1961 params.partition_file = argv[cnt]; in parseArg()
1969 if (strcmp(argv[cnt], "--edge") == 0) { in parseArg()
1970 cnt++; in parseArg()
1971 if (cnt >= argc) in parseArg()
1973 if (strcmp(argv[cnt], "equal") == 0) in parseArg()
1975 else if (strcmp(argv[cnt], "scale") == 0) in parseArg()
1977 else if (strcmp(argv[cnt], "unlink") == 0) in parseArg()
1983 if (strcmp(argv[cnt], "-rcluster") == 0 || strcmp(argv[cnt], "--rcluster") == 0) { in parseArg()
1984 cnt++; in parseArg()
1985 if (cnt >= argc) in parseArg()
1987 params.partfinder_rcluster = convert_double(argv[cnt]); in parseArg()
1993 if (strcmp(argv[cnt], "-rclusterf") == 0 || strcmp(argv[cnt], "--rclusterf") == 0) { in parseArg()
1994 cnt++; in parseArg()
1995 if (cnt >= argc) in parseArg()
1997 params.partfinder_rcluster = convert_double(argv[cnt]); in parseArg()
2004 … if (strcmp(argv[cnt], "-rcluster-max") == 0 || strcmp(argv[cnt], "--rcluster-max") == 0) { in parseArg()
2005 cnt++; in parseArg()
2006 if (cnt >= argc) in parseArg()
2008 params.partfinder_rcluster_max = convert_int(argv[cnt]); in parseArg()
2018 if (strcmp(argv[cnt], "--merge") == 0) { in parseArg()
2019 if (cnt >= argc-1 || argv[cnt+1][0] == '-') { in parseArg()
2025 cnt++; in parseArg()
2026 if (cnt >= argc) in parseArg()
2028 if (strcmp(argv[cnt], "none") == 0) in parseArg()
2030 else if (strcmp(argv[cnt], "greedy") == 0) in parseArg()
2032 else if (strcmp(argv[cnt], "rcluster") == 0) { in parseArg()
2036 } else if (strcmp(argv[cnt], "rclusterf") == 0) { in parseArg()
2040 } else if (strcmp(argv[cnt], "rcluster") == 0) in parseArg()
2047 if (strcmp(argv[cnt], "--merge-model") == 0) { in parseArg()
2048 cnt++; in parseArg()
2049 if (cnt >= argc) in parseArg()
2051 params.merge_models = argv[cnt]; in parseArg()
2061 if (strcmp(argv[cnt], "--merge-rate") == 0) { in parseArg()
2062 cnt++; in parseArg()
2063 if (cnt >= argc) in parseArg()
2065 params.merge_rates = argv[cnt]; in parseArg()
2075 if (strcmp(argv[cnt], "--merge-log-rate") == 0) { in parseArg()
2080 if (strcmp(argv[cnt], "--merge-normal-rate") == 0) { in parseArg()
2085 if (strcmp(argv[cnt], "-keep_empty_seq") == 0) { in parseArg()
2089 if (strcmp(argv[cnt], "-no_terrace") == 0) { in parseArg()
2094 if (strcmp(argv[cnt], "--terrace") == 0) { in parseArg()
2104 if (strcmp(argv[cnt], "--no-terrace") == 0) { in parseArg()
2109 if (strcmp(argv[cnt], "-sf") == 0) { in parseArg()
2110 cnt++; in parseArg()
2111 if (cnt >= argc) in parseArg()
2113 params.ngs_file = argv[cnt]; in parseArg()
2116 if (strcmp(argv[cnt], "-sm") == 0) { in parseArg()
2117 cnt++; in parseArg()
2118 if (cnt >= argc) in parseArg()
2120 params.ngs_mapped_reads = argv[cnt]; in parseArg()
2123 if (strcmp(argv[cnt], "-ngs_gap") == 0) { in parseArg()
2127 if (strcmp(argv[cnt], "-st") == 0 || strcmp(argv[cnt], "--seqtype") == 0) { in parseArg()
2128 cnt++; in parseArg()
2129 if (cnt >= argc) in parseArg()
2131 string arg = argv[cnt]; in parseArg()
2132 params.sequence_type = argv[cnt]; in parseArg()
2149 if (strcmp(argv[cnt], "-starttree") == 0) { in parseArg()
2150 cnt++; in parseArg()
2151 if (cnt >= argc) in parseArg()
2153 if (strcmp(argv[cnt], "BIONJ") == 0) in parseArg()
2155 else if (strcmp(argv[cnt], "PARS") == 0) in parseArg()
2157 else if (strcmp(argv[cnt], "PLLPARS") == 0) in parseArg()
2164 …if (strcmp(argv[cnt], "-ao") == 0 || strcmp(argv[cnt], "--out-alignment") == 0 || strcmp(argv[cnt]… in parseArg()
2165 cnt++; in parseArg()
2166 if (cnt >= argc) in parseArg()
2168 params.aln_output = argv[cnt]; in parseArg()
2171 if (strcmp(argv[cnt], "-as") == 0) { in parseArg()
2172 cnt++; in parseArg()
2173 if (cnt >= argc) in parseArg()
2175 params.aln_site_list = argv[cnt]; in parseArg()
2178 if (strcmp(argv[cnt], "-an") == 0) { in parseArg()
2179 cnt++; in parseArg()
2180 if (cnt >= argc) in parseArg()
2182 params.ref_seq_name = argv[cnt]; in parseArg()
2185 if (strcmp(argv[cnt], "-af") == 0 || strcmp(argv[cnt], "--out-format") == 0) { in parseArg()
2186 cnt++; in parseArg()
2187 if (cnt >= argc) in parseArg()
2189 if (strcmp(argv[cnt], "phy") == 0) in parseArg()
2191 else if (strcmp(argv[cnt], "fasta") == 0) in parseArg()
2193 else if (strcmp(argv[cnt], "nexus") == 0) in parseArg()
2201 if (strcmp(argv[cnt], "--out-csv") == 0) { in parseArg()
2206 if (strcmp(argv[cnt], "--out-tsv") == 0) { in parseArg()
2211 if (strcmp(argv[cnt], "--figtree") == 0) { in parseArg()
2216 if (strcmp(argv[cnt], "-am") == 0) { in parseArg()
2217 cnt++; in parseArg()
2218 if (cnt >= argc) in parseArg()
2220 params.gap_masked_aln = argv[cnt]; in parseArg()
2223 if (strcmp(argv[cnt], "-ac") == 0) { in parseArg()
2224 cnt++; in parseArg()
2225 if (cnt >= argc) in parseArg()
2227 params.concatenate_aln = argv[cnt]; in parseArg()
2230 if (strcmp(argv[cnt], "-nogap") == 0) { in parseArg()
2234 if (strcmp(argv[cnt], "-noconst") == 0) { in parseArg()
2238 if (strcmp(argv[cnt], "-alninfo") == 0) { in parseArg()
2250 if (strcmp(argv[cnt], "-spr") == 0) { in parseArg()
2255 if (strcmp(argv[cnt], "-krep") == 0) { in parseArg()
2256 cnt++; in parseArg()
2257 if (cnt >= argc) in parseArg()
2259 params.k_representative = convert_int(argv[cnt]); in parseArg()
2262 if (strcmp(argv[cnt], "-pdel") == 0) { in parseArg()
2263 cnt++; in parseArg()
2264 if (cnt >= argc) in parseArg()
2266 params.p_delete = convert_double(argv[cnt]); in parseArg()
2271 if (strcmp(argv[cnt], "-pers") == 0 || strcmp(argv[cnt], "--perturb") == 0) { in parseArg()
2272 cnt++; in parseArg()
2273 if (cnt >= argc) in parseArg()
2275 params.initPS = convert_double(argv[cnt]); in parseArg()
2278 if (strcmp(argv[cnt], "-n") == 0) { in parseArg()
2279 cnt++; in parseArg()
2280 if (cnt >= argc) in parseArg()
2285 params.min_iterations = convert_int(argv[cnt]); in parseArg()
2290 if (strcmp(argv[cnt], "-nparam") == 0) { in parseArg()
2291 cnt++; in parseArg()
2292 if (cnt >= argc) in parseArg()
2294 params.num_param_iterations = convert_int(argv[cnt]); in parseArg()
2300 if (strcmp(argv[cnt], "-nb") == 0) { in parseArg()
2301 cnt++; in parseArg()
2302 if (cnt >= argc) in parseArg()
2304 params.min_iterations = convert_int(argv[cnt]); in parseArg()
2309 if (strcmp(argv[cnt], "--model") == 0 || strcmp(argv[cnt], "-m") == 0) { in parseArg()
2310 cnt++; in parseArg()
2311 if (cnt >= argc) in parseArg()
2313 params.model_name = argv[cnt]; in parseArg()
2316 if (strcmp(argv[cnt], "--init-model") == 0) { in parseArg()
2317 cnt++; in parseArg()
2318 if (cnt >= argc) in parseArg()
2320 params.model_name_init = argv[cnt]; in parseArg()
2323 if (strcmp(argv[cnt], "--loop-model") == 0) { in parseArg()
2324 cnt++; in parseArg()
2325 if (cnt >= argc) in parseArg()
2327 params.model_opt_steps = convert_int(argv[cnt]); in parseArg()
2330 …if (strcmp(argv[cnt], "-mset") == 0 || strcmp(argv[cnt], "--mset") == 0 || strcmp(argv[cnt], "--mo… in parseArg()
2331 cnt++; in parseArg()
2332 if (cnt >= argc) in parseArg()
2334 params.model_set = argv[cnt]; in parseArg()
2337 if (strcmp(argv[cnt], "-madd") == 0 || strcmp(argv[cnt], "--madd") == 0) { in parseArg()
2338 cnt++; in parseArg()
2339 if (cnt >= argc) in parseArg()
2341 params.model_extra_set = argv[cnt]; in parseArg()
2344 …if (strcmp(argv[cnt], "-msub") == 0 || strcmp(argv[cnt], "--msub") == 0 || strcmp(argv[cnt], "--mo… in parseArg()
2345 cnt++; in parseArg()
2346 if (cnt >= argc) in parseArg()
2348 params.model_subset = argv[cnt]; in parseArg()
2351 if (strcmp(argv[cnt], "-mfreq") == 0 || strcmp(argv[cnt], "--freqs") == 0) { in parseArg()
2352 cnt++; in parseArg()
2353 if (cnt >= argc) in parseArg()
2355 params.state_freq_set = argv[cnt]; in parseArg()
2358 …if (strcmp(argv[cnt], "-mrate") == 0 || strcmp(argv[cnt], "--mrate") == 0 || strcmp(argv[cnt], "--… in parseArg()
2359 cnt++; in parseArg()
2360 if (cnt >= argc) in parseArg()
2362 params.ratehet_set = argv[cnt]; in parseArg()
2366 if (strcmp(argv[cnt], "--score-diff") == 0) { in parseArg()
2367 cnt++; in parseArg()
2368 if (cnt >= argc) in parseArg()
2370 if (iEquals(argv[cnt], "all")) in parseArg()
2373 params.score_diff_thres = convert_double(argv[cnt]); in parseArg()
2377 if (strcmp(argv[cnt], "-mdef") == 0 || strcmp(argv[cnt], "--mdef") == 0) { in parseArg()
2378 cnt++; in parseArg()
2379 if (cnt >= argc) in parseArg()
2381 params.model_def_file = argv[cnt]; in parseArg()
2384 if (strcmp(argv[cnt], "--modelomatic") == 0) { in parseArg()
2388 …if (strcmp(argv[cnt], "-mredo") == 0 || strcmp(argv[cnt], "--mredo") == 0 || strcmp(argv[cnt], "--… in parseArg()
2392 if (strcmp(argv[cnt], "-mtree") == 0 || strcmp(argv[cnt], "--mtree") == 0) { in parseArg()
2396 if (strcmp(argv[cnt], "-mretree") == 0) { in parseArg()
2400 if (strcmp(argv[cnt], "-msep") == 0) { in parseArg()
2404 if (strcmp(argv[cnt], "-mwopt") == 0 || strcmp(argv[cnt], "--mix-opt") == 0) { in parseArg()
2408 if (strcmp(argv[cnt], "--opt-rate-mat") == 0) { in parseArg()
2424 if (strcmp(argv[cnt], "-rl") == 0) { in parseArg()
2428 if (strcmp(argv[cnt], "-nr") == 0) { in parseArg()
2429 cnt++; in parseArg()
2430 if (cnt >= argc) in parseArg()
2432 params.mean_rate = convert_double(argv[cnt]); in parseArg()
2437 if (strcmp(argv[cnt], "-mstore") == 0) { in parseArg()
2441 if (strcmp(argv[cnt], "-nni_lh") == 0) { in parseArg()
2445 if (strcmp(argv[cnt], "-lmd") == 0) { in parseArg()
2446 cnt++; in parseArg()
2447 if (cnt >= argc) in parseArg()
2449 params.lambda = convert_double(argv[cnt]); in parseArg()
2455 if (strcmp(argv[cnt], "-lk") == 0) { in parseArg()
2456 cnt++; in parseArg()
2457 if (cnt >= argc) in parseArg()
2459 if (strcmp(argv[cnt], "x86") == 0) in parseArg()
2461 else if (strcmp(argv[cnt], "SSE") == 0) in parseArg()
2463 else if (strcmp(argv[cnt], "AVX") == 0) in parseArg()
2465 else if (strcmp(argv[cnt], "FMA") == 0) in parseArg()
2467 else if (strcmp(argv[cnt], "AVX512") == 0) in parseArg()
2474 if (strcmp(argv[cnt], "-safe") == 0 || strcmp(argv[cnt], "--safe") == 0) { in parseArg()
2479 if (strcmp(argv[cnt], "-safe-seq") == 0) { in parseArg()
2480 cnt++; in parseArg()
2481 if (cnt >= argc) in parseArg()
2483 params.numseq_safe_scaling = convert_int(argv[cnt]); in parseArg()
2489 if (strcmp(argv[cnt], "--kernel-nonrev") == 0) { in parseArg()
2494 if (strcmp(argv[cnt], "-f") == 0) { in parseArg()
2495 cnt++; in parseArg()
2496 if (cnt >= argc) in parseArg()
2498 if (strcmp(argv[cnt], "q") == 0 || strcmp(argv[cnt], "EQ") == 0) in parseArg()
2500 else if (strcmp(argv[cnt], "c") == 0 in parseArg()
2501 || strcmp(argv[cnt], "EM") == 0) in parseArg()
2503 else if (strcmp(argv[cnt], "o") == 0 in parseArg()
2504 || strcmp(argv[cnt], "ES") == 0) in parseArg()
2506 else if (strcmp(argv[cnt], "u") == 0 in parseArg()
2507 || strcmp(argv[cnt], "UD") == 0) in parseArg()
2509 else if (strcmp(argv[cnt], "ry") == 0 in parseArg()
2510 || strcmp(argv[cnt], "RY") == 0) in parseArg()
2512 else if (strcmp(argv[cnt], "ws") == 0 in parseArg()
2513 || strcmp(argv[cnt], "WS") == 0) in parseArg()
2515 else if (strcmp(argv[cnt], "mk") == 0 in parseArg()
2516 || strcmp(argv[cnt], "MK") == 0) in parseArg()
2520 params.freq_type = parseStateFreqDigits(argv[cnt]); in parseArg()
2524 if (strcmp(argv[cnt], "--keep-zero-freq") == 0) { in parseArg()
2529 if (strcmp(argv[cnt], "--min-freq") == 0) { in parseArg()
2530 cnt++; in parseArg()
2531 if (cnt >= argc) in parseArg()
2533 params.min_state_freq = convert_double(argv[cnt]); in parseArg()
2541 if (strcmp(argv[cnt], "--inc-zero-freq") == 0) { in parseArg()
2546 if (strcmp(argv[cnt], "-fs") == 0 || strcmp(argv[cnt], "--site-freq") == 0) { in parseArg()
2549 cnt++; in parseArg()
2550 if (cnt >= argc) in parseArg()
2552 params.site_freq_file = argv[cnt]; in parseArg()
2556 if (strcmp(argv[cnt], "-ft") == 0 || strcmp(argv[cnt], "--tree-freq") == 0) { in parseArg()
2559 cnt++; in parseArg()
2560 if (cnt >= argc) in parseArg()
2562 params.tree_freq_file = argv[cnt]; in parseArg()
2568 if (strcmp(argv[cnt], "-fconst") == 0) { in parseArg()
2569 cnt++; in parseArg()
2570 if (cnt >= argc) in parseArg()
2572 params.freq_const_patterns = argv[cnt]; in parseArg()
2575 if (strcmp(argv[cnt], "--nrate") == 0) { in parseArg()
2576 cnt++; in parseArg()
2577 if (cnt >= argc) in parseArg()
2579 params.num_rate_cats = convert_int(argv[cnt]); in parseArg()
2584 if (strcmp(argv[cnt], "-cmin") == 0 || strcmp(argv[cnt], "--cmin") == 0) { in parseArg()
2585 cnt++; in parseArg()
2586 if (cnt >= argc) in parseArg()
2588 params.min_rate_cats = convert_int(argv[cnt]); in parseArg()
2593 if (strcmp(argv[cnt], "-cmax") == 0 || strcmp(argv[cnt], "--cmax") == 0) { in parseArg()
2594 cnt++; in parseArg()
2595 if (cnt >= argc) in parseArg()
2597 params.max_rate_cats = convert_int(argv[cnt]); in parseArg()
2602 if (strcmp(argv[cnt], "-a") == 0) { in parseArg()
2603 cnt++; in parseArg()
2604 if (cnt >= argc) in parseArg()
2606 params.gamma_shape = convert_double(argv[cnt]); in parseArg()
2612 if (strcmp(argv[cnt], "-amin") == 0 || strcmp(argv[cnt], "--alpha-min") == 0) { in parseArg()
2613 cnt++; in parseArg()
2614 if (cnt >= argc) in parseArg()
2616 params.min_gamma_shape = convert_double(argv[cnt]); in parseArg()
2622 if (strcmp(argv[cnt], "-gmean") == 0 || strcmp(argv[cnt], "--gamma-mean") == 0) { in parseArg()
2626 if (strcmp(argv[cnt], "-gmedian") == 0 || strcmp(argv[cnt], "--gamma-median") == 0) { in parseArg()
2630 if (strcmp(argv[cnt], "-i") == 0) { in parseArg()
2631 cnt++; in parseArg()
2632 if (cnt >= argc) in parseArg()
2634 params.p_invar_sites = convert_double(argv[cnt]); in parseArg()
2639 if (strcmp(argv[cnt], "-optfromgiven") == 0) { in parseArg()
2643 if (strcmp(argv[cnt], "-brent") == 0) { in parseArg()
2647 if (strcmp(argv[cnt], "-jointopt") == 0) { in parseArg()
2651 if (strcmp(argv[cnt], "-brent_ginvar") == 0) { in parseArg()
2655 if (strcmp(argv[cnt], "-fixbr") == 0 || strcmp(argv[cnt], "-blfix") == 0) { in parseArg()
2663 if (strcmp(argv[cnt], "-blscale") == 0) { in parseArg()
2671 if (strcmp(argv[cnt], "-blmin") == 0) { in parseArg()
2672 cnt++; in parseArg()
2673 if (cnt >= argc) in parseArg()
2675 params.min_branch_length = convert_double(argv[cnt]); in parseArg()
2685 if (strcmp(argv[cnt], "-blmax") == 0) { in parseArg()
2686 cnt++; in parseArg()
2687 if (cnt >= argc) in parseArg()
2689 params.max_branch_length = convert_double(argv[cnt]); in parseArg()
2694 if (strcmp(argv[cnt], "--show-lh") == 0) { in parseArg()
2705 if (strcmp(argv[cnt], "-sr") == 0) { in parseArg()
2707 cnt++; in parseArg()
2708 if (cnt >= argc) in parseArg()
2710 params.max_iterations = convert_int(argv[cnt]); in parseArg()
2715 if (strcmp(argv[cnt], "-nm") == 0 || strcmp(argv[cnt], "--nmax") == 0) { in parseArg()
2716 cnt++; in parseArg()
2717 if (cnt >= argc) in parseArg()
2719 params.max_iterations = convert_int(argv[cnt]); in parseArg()
2724 if (strcmp(argv[cnt], "-sc") == 0) { in parseArg()
2725 cnt++; in parseArg()
2726 if (cnt >= argc) in parseArg()
2728 params.stop_confidence = convert_double(argv[cnt]); in parseArg()
2734 if (strcmp(argv[cnt], "--runs") == 0) { in parseArg()
2735 cnt++; in parseArg()
2736 if (cnt >= argc) in parseArg()
2738 params.num_runs = convert_int(argv[cnt]); in parseArg()
2743 if (strcmp(argv[cnt], "-gurobi") == 0) { in parseArg()
2747 if (strcmp(argv[cnt], "-gthreads") == 0) { in parseArg()
2749 cnt++; in parseArg()
2750 if (cnt >= argc) in parseArg()
2752 params.gurobi_threads = convert_int(argv[cnt]); in parseArg()
2757 if (strcmp(argv[cnt], "-b") == 0 || strcmp(argv[cnt], "--boot") == 0 || in parseArg()
2758 strcmp(argv[cnt], "-j") == 0 || strcmp(argv[cnt], "--jack") == 0 || in parseArg()
2759 strcmp(argv[cnt], "-bo") == 0 || strcmp(argv[cnt], "--bonly") == 0) { in parseArg()
2761 if (strcmp(argv[cnt], "-bo") == 0 || strcmp(argv[cnt], "--bonly") == 0) in parseArg()
2765 …if ((strcmp(argv[cnt], "-j") == 0 || strcmp(argv[cnt], "--jack") == 0) && params.jackknife_prop ==… in parseArg()
2767 cnt++; in parseArg()
2768 if (cnt >= argc) in parseArg()
2770 params.num_bootstrap_samples = convert_int(argv[cnt]); in parseArg()
2779 …if (strcmp(argv[cnt], "--bsam") == 0 || strcmp(argv[cnt], "-bsam") == 0 || strcmp(argv[cnt], "--sa… in parseArg()
2780 cnt++; in parseArg()
2781 if (cnt >= argc) in parseArg()
2783 params.bootstrap_spec = argv[cnt]; in parseArg()
2788 if (strcmp(argv[cnt], "--subsample") == 0) { in parseArg()
2789 cnt++; in parseArg()
2790 if (cnt >= argc) in parseArg()
2792 params.subsampling = convert_int(argv[cnt]); in parseArg()
2796 if (strcmp(argv[cnt], "--subsample-seed") == 0) { in parseArg()
2797 cnt++; in parseArg()
2798 if (cnt >= argc) in parseArg()
2800 params.subsampling_seed = convert_int(argv[cnt]); in parseArg()
2805 if (strcmp(argv[cnt], "--tbe") == 0) { in parseArg()
2810 if (strcmp(argv[cnt], "--tbe-raw") == 0) { in parseArg()
2816 if (strcmp(argv[cnt], "-bc") == 0 || strcmp(argv[cnt], "--bcon") == 0) { in parseArg()
2819 cnt++; in parseArg()
2820 if (cnt >= argc) in parseArg()
2822 params.num_bootstrap_samples = convert_int(argv[cnt]); in parseArg()
2829 if (strcmp(argv[cnt], "-iqppars") == 0) { in parseArg()
2833 if (strcmp(argv[cnt], "-iqp") == 0) { in parseArg()
2837 if (strcmp(argv[cnt], "-wct") == 0) { in parseArg()
2842 if (strcmp(argv[cnt], "-wt") == 0 || strcmp(argv[cnt], "--treels") == 0) { in parseArg()
2847 if (strcmp(argv[cnt], "-wdt") == 0) { in parseArg()
2852 if (strcmp(argv[cnt], "-wtc") == 0) { in parseArg()
2858 if (strcmp(argv[cnt], "-wt2") == 0) { in parseArg()
2864 if (strcmp(argv[cnt], "-wt3") == 0) { in parseArg()
2870 if (strcmp(argv[cnt], "-wbl") == 0) { in parseArg()
2874 if (strcmp(argv[cnt], "-wit") == 0) { in parseArg()
2879 if (strcmp(argv[cnt], "--write-branches") == 0) { in parseArg()
2888 if (strcmp(argv[cnt], "-rf_all") == 0 || strcmp(argv[cnt], "--tree-dist-all") == 0) { in parseArg()
2892 if (strcmp(argv[cnt], "-rf_adj") == 0) { in parseArg()
2896 if (strcmp(argv[cnt], "-rf") == 0 || strcmp(argv[cnt], "--tree-dist") == 0) { in parseArg()
2898 cnt++; in parseArg()
2899 if (cnt >= argc) in parseArg()
2901 params.second_tree = argv[cnt]; in parseArg()
2904 if (strcmp(argv[cnt], "-rf1") == 0 || strcmp(argv[cnt], "--tree-dist1") == 0) { in parseArg()
2907 cnt++; in parseArg()
2908 if (cnt >= argc) in parseArg()
2910 params.second_tree = argv[cnt]; in parseArg()
2913 if (strcmp(argv[cnt], "-rf2") == 0 || strcmp(argv[cnt], "--tree-dist2") == 0) { in parseArg()
2915 cnt++; in parseArg()
2916 if (cnt >= argc) in parseArg()
2918 params.second_tree = argv[cnt]; in parseArg()
2922 if (strcmp(argv[cnt], "--normalize-dist") == 0) { in parseArg()
2927 if (strcmp(argv[cnt], "-aLRT") == 0) { in parseArg()
2928 cnt++; in parseArg()
2929 if (cnt + 1 >= argc) in parseArg()
2931 params.aLRT_threshold = convert_int(argv[cnt]); in parseArg()
2934 cnt++; in parseArg()
2935 params.aLRT_replicates = convert_int(argv[cnt]); in parseArg()
2941 if (strcmp(argv[cnt], "-alrt") == 0 || strcmp(argv[cnt], "--alrt") == 0) { in parseArg()
2942 cnt++; in parseArg()
2943 if (cnt >= argc) in parseArg()
2945 int reps = convert_int(argv[cnt]); in parseArg()
2955 if (strcmp(argv[cnt], "-abayes") == 0 || strcmp(argv[cnt], "--abayes") == 0) { in parseArg()
2959 if (strcmp(argv[cnt], "-lbp") == 0 || strcmp(argv[cnt], "--lbp") == 0) { in parseArg()
2960 cnt++; in parseArg()
2961 if (cnt >= argc) in parseArg()
2963 params.localbp_replicates = convert_int(argv[cnt]); in parseArg()
2969 if (strcmp(argv[cnt], "-wsl") == 0 || strcmp(argv[cnt], "--sitelh") == 0) { in parseArg()
2974 if (strcmp(argv[cnt], "-wpl") == 0 || strcmp(argv[cnt], "--partlh") == 0) { in parseArg()
2979 if (strcmp(argv[cnt], "-wslg") == 0 || strcmp(argv[cnt], "-wslr") == 0) { in parseArg()
2984 if (strcmp(argv[cnt], "-wslm") == 0) { in parseArg()
2988 if (strcmp(argv[cnt], "-wslmr") == 0 || strcmp(argv[cnt], "-wslrm") == 0) { in parseArg()
2993 if (strcmp(argv[cnt], "-wspr") == 0) { in parseArg()
2998 if (strcmp(argv[cnt], "-wspm") == 0) { in parseArg()
3002 if (strcmp(argv[cnt], "-wspmr") == 0 || strcmp(argv[cnt], "-wsprm") == 0) { in parseArg()
3007 if (strcmp(argv[cnt], "-asr") == 0 || strcmp(argv[cnt], "--ancestral") == 0) { in parseArg()
3013 if (strcmp(argv[cnt], "-asr-min") == 0 || strcmp(argv[cnt], "--asr-min") == 0) { in parseArg()
3014 cnt++; in parseArg()
3015 if (cnt >= argc) in parseArg()
3018 params.min_ancestral_prob = convert_double(argv[cnt]); in parseArg()
3024 if (strcmp(argv[cnt], "-asr-joint") == 0) { in parseArg()
3030 if (strcmp(argv[cnt], "-wsr") == 0 || strcmp(argv[cnt], "--rate") == 0) { in parseArg()
3035 if (strcmp(argv[cnt], "--mlrate") == 0) { in parseArg()
3040 if (strcmp(argv[cnt], "-wsptrees") == 0) { in parseArg()
3044 if (strcmp(argv[cnt], "-wsf") == 0) { in parseArg()
3048 if (strcmp(argv[cnt], "--freq-max") == 0 || strcmp(argv[cnt], "-fmax") == 0) { in parseArg()
3052 if (strcmp(argv[cnt], "-wba") == 0) { in parseArg()
3056 if (strcmp(argv[cnt], "-wbsf") == 0) { in parseArg()
3060 if (strcmp(argv[cnt], "-wsa") == 0) { in parseArg()
3064 if (strcmp(argv[cnt], "-wtl") == 0) { in parseArg()
3068 if (strcmp(argv[cnt], "-wpi") == 0) { in parseArg()
3073 if (strcmp(argv[cnt], "-wca") == 0) { in parseArg()
3078 if (strcmp(argv[cnt], "-wsplits") == 0) { in parseArg()
3082 if (strcmp(argv[cnt], "--no-splits.nex") == 0) { in parseArg()
3086 if (strcmp(argv[cnt], "-ns") == 0) { in parseArg()
3087 cnt++; in parseArg()
3088 if (cnt >= argc) in parseArg()
3090 params.whtest_simulations = convert_int(argv[cnt]); in parseArg()
3095 if (strcmp(argv[cnt], "-mr") == 0) { in parseArg()
3096 cnt++; in parseArg()
3097 if (cnt >= argc) in parseArg()
3099 params.rate_file = argv[cnt]; in parseArg()
3102 if (strcmp(argv[cnt], "-cat_mean") == 0) { in parseArg()
3106 if (strcmp(argv[cnt], "-cat_nolog") == 0) { in parseArg()
3110 if (strcmp(argv[cnt], "-cat_site") == 0) { in parseArg()
3114 if (strcmp(argv[cnt], "-tina") == 0) { in parseArg()
3119 if (strcmp(argv[cnt], "-pval") == 0) { in parseArg()
3120 cnt++; in parseArg()
3121 if (cnt >= argc) in parseArg()
3123 params.gene_pvalue_file = argv[cnt]; in parseArg()
3126 if (strcmp(argv[cnt], "-nnitest") == 0) { in parseArg()
3130 if (strcmp(argv[cnt], "-anni") == 0) { in parseArg()
3134 if (strcmp(argv[cnt], "-nnicut") == 0) { in parseArg()
3139 if (strcmp(argv[cnt], "-nnichi2") == 0) { in parseArg()
3143 if (strcmp(argv[cnt], "-nnicutval") == 0) { in parseArg()
3144 cnt++; in parseArg()
3145 if (cnt >= argc) in parseArg()
3147 params.nni_cutoff = convert_double(argv[cnt]); in parseArg()
3152 if (strcmp(argv[cnt], "-nnisort") == 0) { in parseArg()
3156 if (strcmp(argv[cnt], "-plog") == 0) { in parseArg()
3160 if (strcmp(argv[cnt], "-dmp") == 0) { in parseArg()
3161 cnt++; in parseArg()
3162 if (cnt >= argc) in parseArg()
3164 params.ncbi_taxid = convert_int(argv[cnt]); in parseArg()
3167 if (strcmp(argv[cnt], "-dmplevel") == 0 in parseArg()
3168 || strcmp(argv[cnt], "-dmprank") == 0) { in parseArg()
3169 cnt++; in parseArg()
3170 if (cnt >= argc) in parseArg()
3172 params.ncbi_taxon_level = argv[cnt]; in parseArg()
3175 if (strcmp(argv[cnt], "-dmpignore") == 0) { in parseArg()
3176 cnt++; in parseArg()
3177 if (cnt >= argc) in parseArg()
3179 params.ncbi_ignore_level = argv[cnt]; in parseArg()
3182 if (strcmp(argv[cnt], "-dmpname") == 0) { in parseArg()
3183 cnt++; in parseArg()
3184 if (cnt >= argc) in parseArg()
3186 params.ncbi_names_file = argv[cnt]; in parseArg()
3189 if (strcmp(argv[cnt], "-eco") == 0) { in parseArg()
3190 cnt++; in parseArg()
3191 if (cnt >= argc) in parseArg()
3193 params.eco_dag_file = argv[cnt]; in parseArg()
3196 if (strcmp(argv[cnt], "-k%") == 0) { in parseArg()
3197 cnt++; in parseArg()
3198 if (cnt >= argc) in parseArg()
3201 params.k_percent = convert_int(argv[cnt]); in parseArg()
3204 if (strcmp(argv[cnt], "-diet") == 0) { in parseArg()
3205 cnt++; in parseArg()
3206 if (cnt >= argc) in parseArg()
3208 convert_range(argv[cnt], params.diet_min, params.diet_max, in parseArg()
3213 if (strcmp(argv[cnt], "-up") == 0) { in parseArg()
3217 if (strcmp(argv[cnt], "-upNNI") == 0) { in parseArg()
3220 if (strcmp(argv[cnt], "-upFrac") == 0) { in parseArg()
3221 cnt++; in parseArg()
3222 if (cnt >= argc) in parseArg()
3224 params.upper_bound_frac = convert_double(argv[cnt]); in parseArg()
3226 if (strcmp(argv[cnt], "-ecoR") == 0) { in parseArg()
3227 cnt++; in parseArg()
3228 if (cnt >= argc) in parseArg()
3230 params.eco_run = convert_int(argv[cnt]); in parseArg()
3233 …if (strcmp(argv[cnt], "-bb") == 0 || strcmp(argv[cnt], "-B") == 0 || strcmp(argv[cnt], "--ufboot")… in parseArg()
3234 strcmp(argv[cnt], "-J") == 0 || strcmp(argv[cnt], "--ufjack") == 0) { in parseArg()
3235 …if ((strcmp(argv[cnt], "-J") == 0 || strcmp(argv[cnt], "--ufjack") == 0) && params.jackknife_prop … in parseArg()
3237 cnt++; in parseArg()
3238 if (cnt >= argc) in parseArg()
3243 params.gbo_replicates = convert_int(argv[cnt]); in parseArg()
3252 if (strcmp(argv[cnt], "-beps") == 0 || strcmp(argv[cnt], "--beps") == 0) { in parseArg()
3253 cnt++; in parseArg()
3254 if (cnt >= argc) in parseArg()
3256 params.ufboot_epsilon = convert_double(argv[cnt]); in parseArg()
3261 …if (strcmp(argv[cnt], "-wbt") == 0 || strcmp(argv[cnt], "--wbt") == 0 || strcmp(argv[cnt], "--boot… in parseArg()
3265 if (strcmp(argv[cnt], "-wbtl") == 0 || strcmp(argv[cnt], "--wbtl") == 0) { in parseArg()
3270 if (strcmp(argv[cnt], "-bs") == 0) { in parseArg()
3271 cnt++; in parseArg()
3272 if (cnt >= argc) in parseArg()
3274 params.check_gbo_sample_size = convert_int(argv[cnt]); in parseArg()
3277 if (strcmp(argv[cnt], "-bmax") == 0) { in parseArg()
3278 cnt++; in parseArg()
3279 if (cnt >= argc) in parseArg()
3281 params.max_candidate_trees = convert_int(argv[cnt]); in parseArg()
3284 if (strcmp(argv[cnt], "-bcor") == 0 | strcmp(argv[cnt], "--bcor") == 0) { in parseArg()
3285 cnt++; in parseArg()
3286 if (cnt >= argc) in parseArg()
3288 params.min_correlation = convert_double(argv[cnt]); in parseArg()
3291 if (strcmp(argv[cnt], "--bnni") == 0 || strcmp(argv[cnt], "-bnni") == 0) { in parseArg()
3297 if (strcmp(argv[cnt], "-u2c_nni5") == 0) { in parseArg()
3302 if (strcmp(argv[cnt], "-nstep") == 0 || strcmp(argv[cnt], "--nstep") == 0) { in parseArg()
3303 cnt++; in parseArg()
3304 if (cnt >= argc) in parseArg()
3306 params.step_iterations = convert_int(argv[cnt]); in parseArg()
3313 if (strcmp(argv[cnt], "-boff") == 0) { in parseArg()
3323 if (strcmp(argv[cnt], "--jack-prop") == 0) { in parseArg()
3324 cnt++; in parseArg()
3325 if (cnt >= argc) in parseArg()
3327 params.jackknife_prop = convert_double(argv[cnt]); in parseArg()
3333 if (strcmp(argv[cnt], "-mem") == 0 || strcmp(argv[cnt], "--mem") == 0) { in parseArg()
3334 cnt++; in parseArg()
3335 if (cnt >= argc) in parseArg()
3339 double mem = convert_double(argv[cnt], end_pos); in parseArg()
3342 if (argv[cnt][end_pos] == 'G') { in parseArg()
3344 } else if (argv[cnt][end_pos] == 'M') { in parseArg()
3346 } else if (argv[cnt][end_pos] == '%'){ in parseArg()
3357 if (strcmp(argv[cnt], "--save-mem-buffer") == 0) { in parseArg()
3361 if (strcmp(argv[cnt], "--no-save-mem-buffer") == 0) { in parseArg()
3369 if (strcmp(argv[cnt], "-nodiff") == 0) { in parseArg()
3373 if (strcmp(argv[cnt], "-treediff") == 0) { in parseArg()
3377 if (strcmp(argv[cnt], "-norell") == 0) { in parseArg()
3381 if (strcmp(argv[cnt], "-elw") == 0) { in parseArg()
3385 if (strcmp(argv[cnt], "-noweight") == 0) { in parseArg()
3389 if (strcmp(argv[cnt], "-nomore") == 0) { in parseArg()
3393 if (strcmp(argv[cnt], "-bweight") == 0) { in parseArg()
3397 if (strcmp(argv[cnt], "-bmore") == 0) { in parseArg()
3401 if (strcmp(argv[cnt], "-gz") == 0) { in parseArg()
3405 if (strcmp(argv[cnt], "-newheu") == 0) { in parseArg()
3410 if (strcmp(argv[cnt], "-maxtime") == 0) { in parseArg()
3411 cnt++; in parseArg()
3412 if (cnt >= argc) in parseArg()
3414 params.maxtime = convert_double(argv[cnt]); in parseArg()
3419 if (strcmp(argv[cnt], "--ninit") == 0 || strcmp(argv[cnt], "-ninit") == 0) { in parseArg()
3420 cnt++; in parseArg()
3421 if (cnt >= argc) in parseArg()
3423 params.numInitTrees = convert_int(argv[cnt]); in parseArg()
3430 if (strcmp(argv[cnt], "-fast") == 0 || strcmp(argv[cnt], "--fast") == 0) { in parseArg()
3442 if (strcmp(argv[cnt], "-fss") == 0) { in parseArg()
3447 if (strcmp(argv[cnt], "--stable-thres") == 0) { in parseArg()
3448 cnt++; in parseArg()
3449 if (cnt >= argc) in parseArg()
3451 params.stableSplitThreshold = convert_double(argv[cnt]); in parseArg()
3454 if (strcmp(argv[cnt], "-ff") == 0) { in parseArg()
3459 if (strcmp(argv[cnt], "-tabu") == 0) { in parseArg()
3466 if (strcmp(argv[cnt], "--adt-pert") == 0) { in parseArg()
3475 if (strcmp(argv[cnt], "-memcheck") == 0) { in parseArg()
3480 if (strcmp(argv[cnt], "--ntop") == 0 || strcmp(argv[cnt], "-ntop") == 0) { in parseArg()
3481 cnt++; in parseArg()
3482 if (cnt >= argc) in parseArg()
3484 params.numNNITrees = convert_int(argv[cnt]); in parseArg()
3487 if (strcmp(argv[cnt], "--num-sup-trees") == 0) { in parseArg()
3488 cnt++; in parseArg()
3489 if (cnt >= argc) in parseArg()
3491 params.numSupportTrees = convert_int(argv[cnt]); in parseArg()
3494 if (strcmp(argv[cnt], "-fixai") == 0) { in parseArg()
3495 cnt++; in parseArg()
3496 if (cnt >= argc) in parseArg()
3498 params.alpha_invar_file = argv[cnt]; in parseArg()
3502 if (strcmp(argv[cnt], "--opt-gamma-inv") == 0) { in parseArg()
3507 if (strcmp(argv[cnt], "--no-opt-gamma-inv") == 0) { in parseArg()
3512 if (strcmp(argv[cnt], "--opt-gammai-fast") == 0) { in parseArg()
3518 if (strcmp(argv[cnt], "--opt-gammai-kb") == 0) { in parseArg()
3524 if (strcmp(argv[cnt], "--adaptive-eps") == 0) { in parseArg()
3528 if (strcmp(argv[cnt], "--rand-alpha") == 0) { in parseArg()
3533 if (strcmp(argv[cnt], "-eai") == 0) { in parseArg()
3537 if (strcmp(argv[cnt], "-poplim") == 0) { in parseArg()
3538 cnt++; in parseArg()
3539 if (cnt >= argc) in parseArg()
3541 params.maxCandidates = convert_int(argv[cnt]); in parseArg()
3544 if (strcmp(argv[cnt], "--nbest") == 0 ||strcmp(argv[cnt], "-nbest") == 0) { in parseArg()
3545 cnt++; in parseArg()
3546 if (cnt >= argc) in parseArg()
3548 params.popSize = convert_int(argv[cnt]); in parseArg()
3552 if (strcmp(argv[cnt], "-beststart") == 0) { in parseArg()
3554 cnt++; in parseArg()
3555 if (cnt >= argc) in parseArg()
3557 params.binary_aln_file = argv[cnt]; in parseArg()
3560 if (strcmp(argv[cnt], "-pll") == 0) { in parseArg()
3565 if (strcmp(argv[cnt], "-me") == 0 || strcmp(argv[cnt], "--epsilon") == 0) { in parseArg()
3566 cnt++; in parseArg()
3567 if (cnt >= argc) in parseArg()
3569 params.modelEps = convert_double(argv[cnt]); in parseArg()
3577 if (strcmp(argv[cnt], "--mf-epsilon") == 0) { in parseArg()
3578 cnt++; in parseArg()
3579 if (cnt >= argc) in parseArg()
3581 params.modelfinder_eps = convert_double(argv[cnt]); in parseArg()
3589 if (strcmp(argv[cnt], "-pars_ins") == 0) { in parseArg()
3593 if (strcmp(argv[cnt], "-allnni") == 0 || strcmp(argv[cnt], "--allnni") == 0) { in parseArg()
3598 if (strcmp(argv[cnt], "-snni") == 0) { in parseArg()
3607 if (strcmp(argv[cnt], "-iqpnni") == 0) { in parseArg()
3615 if (strcmp(argv[cnt], "--nstop") == 0 || strcmp(argv[cnt], "-nstop") == 0) { in parseArg()
3618 cnt++; in parseArg()
3619 if (cnt >= argc) in parseArg()
3621 params.unsuccess_iteration = convert_int(argv[cnt]); in parseArg()
3627 if (strcmp(argv[cnt], "-lsbran") == 0) { in parseArg()
3631 if (strcmp(argv[cnt], "-manuel") == 0) { in parseArg()
3635 if (strcmp(argv[cnt], "-parsbran") == 0) { in parseArg()
3639 if (strcmp(argv[cnt], "-bayesbran") == 0) { in parseArg()
3643 if (strcmp(argv[cnt], "-fivebran") == 0 in parseArg()
3644 || strcmp(argv[cnt], "-nni5") == 0) { in parseArg()
3649 if (strcmp(argv[cnt], "-onebran") == 0 in parseArg()
3650 || strcmp(argv[cnt], "-nni1") == 0) { in parseArg()
3656 if (strcmp(argv[cnt], "-nni-eval") == 0) { in parseArg()
3657 cnt++; in parseArg()
3658 if (cnt >= argc) in parseArg()
3660 params.nni5_num_eval = convert_int(argv[cnt]); in parseArg()
3666 if (strcmp(argv[cnt], "-bl-eval") == 0) { in parseArg()
3667 cnt++; in parseArg()
3668 if (cnt >= argc) in parseArg()
3670 params.brlen_num_traversal = convert_int(argv[cnt]); in parseArg()
3676 if (strcmp(argv[cnt], "-smooth") == 0) { in parseArg()
3677 cnt++; in parseArg()
3678 if (cnt >= argc) in parseArg()
3680 params.numSmoothTree = convert_int(argv[cnt]); in parseArg()
3683 if (strcmp(argv[cnt], "-lsnni") == 0) { in parseArg()
3687 if (strcmp(argv[cnt], "-lsvar") == 0) { in parseArg()
3688 cnt++; in parseArg()
3689 if (cnt >= argc) in parseArg()
3691 if (strcmp(argv[cnt], "o") == 0 in parseArg()
3692 || strcmp(argv[cnt], "ols") == 0) { in parseArg()
3696 if (strcmp(argv[cnt], "ft") == 0 in parseArg()
3697 || strcmp(argv[cnt], "first_taylor") == 0) { in parseArg()
3701 if (strcmp(argv[cnt], "fm") == 0 in parseArg()
3702 || strcmp(argv[cnt], "fitch_margoliash") == 0) { in parseArg()
3706 if (strcmp(argv[cnt], "st") == 0 in parseArg()
3707 || strcmp(argv[cnt], "second_taylor") == 0) { in parseArg()
3711 if (strcmp(argv[cnt], "p") == 0 in parseArg()
3712 || strcmp(argv[cnt], "pauplin") == 0) { in parseArg()
3719 if (strcmp(argv[cnt], "-eps") == 0) { in parseArg()
3720 cnt++; in parseArg()
3721 if (cnt >= argc) in parseArg()
3723 params.loglh_epsilon = convert_double(argv[cnt]); in parseArg()
3726 if (strcmp(argv[cnt], "-pb") == 0) { // Enable parsimony branch length estimation in parseArg()
3730 if (strcmp(argv[cnt], "-x") == 0) { in parseArg()
3731 cnt++; in parseArg()
3732 if (cnt >= argc) in parseArg()
3734 params.iteration_multiple = convert_int(argv[cnt]); in parseArg()
3737 if (strcmp(argv[cnt], "-sp_iter") == 0) { in parseArg()
3738 cnt++; in parseArg()
3739 if (cnt >= argc) in parseArg()
3741 params.speedup_iter = convert_int(argv[cnt]); in parseArg()
3744 if (strcmp(argv[cnt], "-avh") == 0) { in parseArg()
3745 cnt++; in parseArg()
3746 if (cnt >= argc) in parseArg()
3748 params.avh_test = convert_int(argv[cnt]); in parseArg()
3751 if (strcmp(argv[cnt], "-bootlh") == 0) { in parseArg()
3752 cnt++; in parseArg()
3753 if (cnt >= argc) in parseArg()
3755 params.bootlh_test = convert_int(argv[cnt]); in parseArg()
3758 if (strcmp(argv[cnt], "-bootpart") == 0) { in parseArg()
3759 cnt++; in parseArg()
3760 if (cnt >= argc) in parseArg()
3762 params.bootlh_partitions = argv[cnt]; in parseArg()
3765 if (strcmp(argv[cnt], "-AIC") == 0) { in parseArg()
3769 if (strcmp(argv[cnt], "-AICc") == 0 || strcmp(argv[cnt], "-AICC") == 0) { in parseArg()
3773 if (strcmp(argv[cnt], "-merit") == 0 || strcmp(argv[cnt], "--merit") == 0) { in parseArg()
3774 cnt++; in parseArg()
3775 if (cnt >= argc) in parseArg()
3777 if (strcmp(argv[cnt], "AIC") == 0) in parseArg()
3779 else if (strcmp(argv[cnt], "AICc") == 0 || strcmp(argv[cnt], "AICC") == 0) in parseArg()
3781 else if (strcmp(argv[cnt], "BIC") == 0) in parseArg()
3786 if (strcmp(argv[cnt], "-ms") == 0) { in parseArg()
3787 cnt++; in parseArg()
3788 if (cnt >= argc) in parseArg()
3790 params.model_test_sample_size = convert_int(argv[cnt]); in parseArg()
3793 if (strcmp(argv[cnt], "-nt") == 0 || strcmp(argv[cnt], "-c") == 0 || in parseArg()
3794 strcmp(argv[cnt], "-T") == 0 || strcmp(argv[cnt], "--threads") == 0) { in parseArg()
3795 cnt++; in parseArg()
3796 if (cnt >= argc) in parseArg()
3798 if (iEquals(argv[cnt], "AUTO")) in parseArg()
3801 params.num_threads = convert_int(argv[cnt]); in parseArg()
3808 if (strcmp(argv[cnt], "-ntmax") == 0 || strcmp(argv[cnt], "--threads-max") == 0) { in parseArg()
3809 cnt++; in parseArg()
3810 if (cnt >= argc) in parseArg()
3812 params.num_threads_max = convert_int(argv[cnt]); in parseArg()
3818 if (strcmp(argv[cnt], "--thread-model") == 0) { in parseArg()
3823 if (strcmp(argv[cnt], "--thread-site") == 0) { in parseArg()
3836 if (strcmp(argv[cnt], "-ct") == 0) { in parseArg()
3840 if (strcmp(argv[cnt], "--sprrad") == 0 || strcmp(argv[cnt], "--radius") == 0) { in parseArg()
3841 cnt++; in parseArg()
3842 if (cnt >= argc) in parseArg()
3844 params.sprDist = convert_int(argv[cnt]); in parseArg()
3848 if (strcmp(argv[cnt], "--mpcost") == 0) { in parseArg()
3849 cnt++; in parseArg()
3850 if (cnt >= argc) in parseArg()
3852 params.sankoff_cost_file = argv[cnt]; in parseArg()
3856 if (strcmp(argv[cnt], "-no_rescale_gamma_invar") == 0) { in parseArg()
3861 if (strcmp(argv[cnt], "-wsi") == 0) { in parseArg()
3866 if (strcmp(argv[cnt], "--no-seq-comp") == 0) { in parseArg()
3871 …if (strcmp(argv[cnt], "-t") == 0 || strcmp(argv[cnt], "-te") == 0 || strcmp(argv[cnt], "--tree") =… in parseArg()
3872 if (strcmp(argv[cnt], "-te") == 0) { in parseArg()
3879 cnt++; in parseArg()
3880 if (cnt >= argc) in parseArg()
3882 if (strcmp(argv[cnt], "BIONJ") == 0 || strcmp(argv[cnt], "NJ") == 0) in parseArg()
3884 else if (strcmp(argv[cnt], "PARS") == 0) in parseArg()
3886 else if (strcmp(argv[cnt], "PLLPARS") == 0) in parseArg()
3888 else if (strcmp(argv[cnt], "RANDOM") == 0 || strcmp(argv[cnt], "RAND") == 0) in parseArg()
3891 params.user_file = argv[cnt]; in parseArg()
3898 if (strcmp(argv[cnt], "--no-ml-tree") == 0) { in parseArg()
3903 if (strcmp(argv[cnt], "--tree-fix") == 0) { in parseArg()
3911 if (strcmp(argv[cnt], "-g") == 0) { in parseArg()
3912 cnt++; in parseArg()
3913 if (cnt >= argc) in parseArg()
3915 params.constraint_tree_file = argv[cnt]; in parseArg()
3919 if (strcmp(argv[cnt], "-lmap") == 0 || strcmp(argv[cnt], "--lmap") == 0) { in parseArg()
3920 cnt++; in parseArg()
3921 if (cnt >= argc) in parseArg()
3923 if (iEquals(argv[cnt], "ALL")) { in parseArg()
3926 params.lmap_num_quartets = convert_int64(argv[cnt]); in parseArg()
3933 if (strcmp(argv[cnt], "-lmclust") == 0 || strcmp(argv[cnt], "--lmclust") == 0) { in parseArg()
3934 cnt++; in parseArg()
3935 if (cnt >= argc) in parseArg()
3937 params.lmap_cluster_file = argv[cnt]; in parseArg()
3946 if (strcmp(argv[cnt], "-wql") == 0 || strcmp(argv[cnt], "--quartetlh") == 0) { in parseArg()
3951 if (strcmp(argv[cnt], "-mixlen") == 0) { in parseArg()
3952 cnt++; in parseArg()
3953 if (cnt >= argc) in parseArg()
3955 params.num_mixlen = convert_int(argv[cnt]); in parseArg()
3961 if (strcmp(argv[cnt], "--link-alpha") == 0) { in parseArg()
3966 if (strcmp(argv[cnt], "--link-model") == 0) { in parseArg()
3971 if (strcmp(argv[cnt], "--model-joint") == 0) { in parseArg()
3972 cnt++; in parseArg()
3973 if (cnt >= argc) in parseArg()
3975 params.model_joint = argv[cnt]; in parseArg()
3980 if (strcmp(argv[cnt], "--unlink-tree") == 0) { in parseArg()
3986 if (strcmp(argv[cnt], "-redo") == 0 || strcmp(argv[cnt], "--redo") == 0) { in parseArg()
3993 …if (strcmp(argv[cnt], "-tredo") == 0 || strcmp(argv[cnt], "--tredo") == 0 || strcmp(argv[cnt], "--… in parseArg()
3998 if (strcmp(argv[cnt], "-undo") == 0 || strcmp(argv[cnt], "--undo") == 0) { in parseArg()
4003 if (strcmp(argv[cnt], "-cptime") == 0 || strcmp(argv[cnt], "--cptime") == 0) { in parseArg()
4004 cnt++; in parseArg()
4005 if (cnt >= argc) in parseArg()
4007 params.checkpoint_dump_interval = convert_int(argv[cnt]); in parseArg()
4011 if (strcmp(argv[cnt], "--no-log") == 0) { in parseArg()
4016 if (strcmp(argv[cnt], "--no-treefile") == 0) { in parseArg()
4020 if (strcmp(argv[cnt], "--no-iqtree") == 0) { in parseArg()
4024 if (strcmp(argv[cnt], "--no-outfiles") == 0) { in parseArg()
4031 if (strcmp(argv[cnt], "--scaling-squaring") == 0) { in parseArg()
4035 if (strcmp(argv[cnt], "--eigenlib") == 0) { in parseArg()
4039 if (strcmp(argv[cnt], "--eigen") == 0) { in parseArg()
4043 if (strcmp(argv[cnt], "--lie-markov") == 0) { in parseArg()
4047 if (strcmp(argv[cnt], "--no-uniqueseq") == 0) { in parseArg()
4053 if (strcmp(argv[cnt], "--dating") == 0) { in parseArg()
4054 cnt++; in parseArg()
4055 if (cnt >= argc) in parseArg()
4057 params.dating_method = argv[cnt]; in parseArg()
4063 if (strcmp(argv[cnt], "--date") == 0) { in parseArg()
4064 cnt++; in parseArg()
4065 if (cnt >= argc) in parseArg()
4069 params.date_file = argv[cnt]; in parseArg()
4073 if (strcmp(argv[cnt], "--date-tip") == 0) { in parseArg()
4074 cnt++; in parseArg()
4075 if (cnt >= argc) in parseArg()
4079 params.date_tip = argv[cnt]; in parseArg()
4083 if (strcmp(argv[cnt], "--date-root") == 0) { in parseArg()
4084 cnt++; in parseArg()
4085 if (cnt >= argc) in parseArg()
4089 params.date_root = argv[cnt]; in parseArg()
4093 if (strcmp(argv[cnt], "--date-no-outgroup") == 0) { in parseArg()
4098 if (strcmp(argv[cnt], "--date-outgroup") == 0) { in parseArg()
4103 if (strcmp(argv[cnt], "--date-ci") == 0) { in parseArg()
4104 cnt++; in parseArg()
4105 if (cnt >= argc) in parseArg()
4107 params.date_replicates = convert_int(argv[cnt]); in parseArg()
4113 if (strcmp(argv[cnt], "--clock-sd") == 0) { in parseArg()
4114 cnt++; in parseArg()
4115 if (cnt >= argc) in parseArg()
4117 params.clock_stddev = convert_double(argv[cnt]); in parseArg()
4123 if (strcmp(argv[cnt], "--date-outlier") == 0) { in parseArg()
4124 cnt++; in parseArg()
4125 if (cnt >= argc) in parseArg()
4127 params.date_outlier = convert_double(argv[cnt]); in parseArg()
4133 if (strcmp(argv[cnt], "--date-debug") == 0) { in parseArg()
4139 if (strcmp(argv[cnt], "--date-options") == 0) { in parseArg()
4140 cnt++; in parseArg()
4141 if (cnt >= argc) in parseArg()
4143 params.dating_options = argv[cnt]; in parseArg()
4147 if (argv[cnt][0] == '-') { in parseArg()
4149 err += argv[cnt]; in parseArg()
4154 params.user_file = argv[cnt]; in parseArg()
4156 params.out_file = argv[cnt]; in parseArg()
4174 err += argv[cnt]; in parseArg()