Additional Information: 1. ALL likelihood values are RAxML GAMMA Likelihood values. 2. Models for RAxML - GAMMA complete inference under GAMMA - CAT-50 complete inference with 50 distinct rate categories - CAT-50+R_GAMMA complete inference with 50 distinct rate categories + refinement under GAMMA - CAT-25 complete inference with 25 distinct rate categories - CAT-50+R_GAMMA complete inference with 25 distinct rate categories + refinement under GAMMA 3. Times and Likelihoods for RAxML models are averages over 5 (large datasets) or 10 (small dattasets) randomized parsimony starting trees. 4. Values for IQPNNI and PHYML are on the BIONJ starting of those programs, i.e. no avverages. 5. Average RF-distances to the respective GAMMA-trees have been determined for each individual run (each starting tree). Note that ALL RAxML, IQPNNI, and PHYML Likelihood values have been obtained by invoking RAxML branch length and model parameter optimization under the GAMMA model. Datasets: 73_OLAF: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -28371.667567 -28372.824933 -28371.809743 -28372.841792 -28371.742160 | -28375.607325 -28375.025722 Avg Times: 525.242607 135.061057 195.242566 125.745846 188.939410 | 106.000000 135.000000 Avg RF-distances: 0.008392 0.006294 0.008392 0.005594 74_OLAF: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -9142.656120 -9142.910435 -9142.910435 -9142.990694 -9142.990694 | -9142.519049 -9142.519049 Avg Times: 140.584823 40.913345 58.227305 40.678028 57.864333 | 51.000000 50.000000 Avg RF-distances: 0.030769 0.030769 0.029371 0.029371 104_OLAF: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -11355.028158 -11361.463681 -11352.773468 -11359.387952 -11351.706676 | -11362.052307 -11367.161506 Avg Times: 259.163147 97.392875 197.037757 87.204641 176.831679 | 69.000000 126.000000 Avg RF-distances: 0.118537 0.101463 0.113659 0.098049 128_OLAF: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -107890.071852 -107887.078258 -107860.992448 -107887.265354 -107861.137280 | -107891.69 -107860.515095 Avg Times: 9705.124529 1109.599651 2167.221271 1111.833832 2224.485401 | 1108.000000 1024.000000 Avg RF-distances: 0.014625 0.014625 0.016996 0.016996 144_OLAF: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -32003.792226 -32004.239136 -32000.115161 -32004.342791 -32000.366662 | -32018.26 -32026.935124 Avg Times: 1336.099539 309.823680 613.497068 306.911485 598.234604 | 439.000000 316.000000 Avg RF-distances: 0.054386 0.052281 0.055789 0.055088 178_OLAF: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -55265.570596 -55265.748608 -55255.511914 -55265.698290 -55255.481148 | -55263.173 -55254.485756 Avg Times: 3273.585485 748.735329 1461.274875 690.330955 1365.133275 | 531.000000 553.000000 Avg RF-distances: 0.023796 0.024646 0.026346 0.026062 180_OLAF: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -23663.910921 -23675.339301 -23661.484701 -23673.182907 -23661.268296 | -23738.079 -23713.800457 Avg Times: 1878.388129 625.251886 928.104790 576.008245 816.476454 | 212.000000 634.000000 Avg RF-distances: 0.051261 0.047339 0.048179 0.046499 101_SC: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -64847.333825 -64862.764330 -64857.550072 -64860.902707 -64855.549916 | -65048.14 -64954.588308 Avg Times: 3985.446130 447.528717 957.301125 463.000631 976.491532 | 475.000000 554.000000 Avg RF-distances: 0.103518 0.091960 0.098492 0.084925 150_SC: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -39654.814380 -39659.702177 -39653.951112 -39656.599124 -39653.361531 | -39778.627 -39742.988939 Avg Times: 2387.090414 556.651795 1083.907280 566.699293 907.424802 | 511.000000 583.000000 Avg RF-distances: 0.049832 0.034680 0.040404 0.032323 150_ARB: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -69847.987107 -69845.720354 -69845.324248 -69846.633468 -69845.766671 | -69870.219 -69877.623953 Avg Times: 5500.465048 783.608833 1226.893025 793.036085 1333.258577 | 1722.000000 1262.000000 Avg RF-distances: 0.012458 0.012795 0.013805 0.014478 193_VINH: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -62334.412860 -62336.920675 -62333.327249 -62338.858214 -62333.983183 | -62399.032 -62372.646040 Avg Times: 1769.811271 746.986298 974.718728 696.237083 970.983305 | 251.000000 636.000000 Avg RF-distances: 0.114099 0.111488 0.117755 0.112272 200_ARB: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -93265.375555 -93258.654729 -93256.058407 -93259.015870 -93257.059145 | -93315.08 -93283.710613 Avg Times: 11051.989856 1467.935311 2937.845270 1501.681938 2775.988535 | 2219.000000 1435.000000 Avg RF-distances: 0.042821 0.039043 0.036272 0.034257 218_RDPII: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -134509.656054 -134530.600174 -134503.541070 -134533.296336 -134507.182368 | -134757.23 -134671.047065 Avg Times: 15004.156364 2569.318305 6467.963030 2547.131385 6466.828105 | 1844.000000 2325.000000 Avg RF-distances: 0.115473 0.101848 0.120092 0.103695 250_ARB: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -115742.993812 -115738.352500 -115732.979773 -115739.890974 -115734.236975 | -115770.831 -115768.856601 Avg Times: 19448.750052 2699.760878 5307.839550 2748.496804 5095.083845 | 2784.000000 2261.000000 Avg RF-distances: 0.029376 0.027163 0.032394 0.028974 500_ARB: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -219664.446619 -219649.098895 -219616.750003 -219639.883499 -219618.895075 | -220452.877 -220040.175678 Avg Times: 127390.842044 19508.775028 45540.702605 17266.126454 39281.299399 | 6009.000000 13058.000000 Avg RF-distances: 0.061384 0.055767 0.057573 0.050351 500_ZILLA: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -86100.941520 -86089.277363 -86084.365335 -86087.153718 -86083.453232 | -86248.348470 -86161.926179 Avg Times: 21131.554064 6056.469123 8540.034553 5084.511854 7010.760278 | 1589.000000 3647.000000 Avg RF-distances: 0.056369 0.050150 0.054162 0.048947 715_CHUCK: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -149033.279822 -149037.832239 -149015.953663 -149034.625674 -149011.478617 | -149930.792 -149510.782297 Avg Times: 29829.156496 5671.251829 11856.896641 6396.490188 12980.957292 | 3639.000000 4883.000000 Avg RF-distances: 0.043868 0.039383 0.043868 0.039804 1000_ARB: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -350191.990871 -349689.661917 -349655.928851 -349683.643635 -349650.545158 | -350721.700 -350627.746623 Avg Times: 479888.165478 59826.077767 148140.267265 58871.837637 165806.934531 | 38232.000000 71810.000000 Avg RF-distances: 0.049574 0.047672 0.051377 0.048072 1663_ARB: Model: GAMMA CAT-50 CAT-50+R_GAMMA CAT-25 CAT-25+R_GAMMA | PHYML IQPNNI Avg Likelihoods: -274181.177470 -274132.769051 -274099.058058 -274120.678319 -274093.527905 | -275057.9383 -274960.436782 Avg Times: 328634.883941 70894.833440 193358.263288 67105.189057 179779.358753 | 15393.000000 54712.000000 Avg RF-distances: 0.088474 0.084637 0.087571 0.084487