IQ-TREE multicore version 1.6.12 for Mac OS X 64-bit built Aug 15 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: NORVEGE.local (AVX512, FMA3, 16 GB RAM) Command: iqtree -s /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta -bb 1000 -nt AUTO Seed: 244917 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Sep 1 09:54:48 2021 Kernel: AVX+FMA - auto-detect threads (8 CPU cores detected) Reading alignment file /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta ... Fasta format detected NOTE: Change sequence name 'Haplotype_1 [192]_MT078946' -> Haplotype_1_[192]_MT078946 NOTE: Change sequence name 'Haplotype_2 [95]_MT078949' -> Haplotype_2_[95]_MT078949 NOTE: Change sequence name 'Haplotype_3 [9]_MT078951' -> Haplotype_3_[9]_MT078951 NOTE: Change sequence name 'Haplotype_4 [41]_MT078952' -> Haplotype_4_[41]_MT078952 NOTE: Change sequence name 'Haplotype_5 [2]_MT078954 (reversed)' -> Haplotype_5_[2]_MT078954 NOTE: Change sequence name 'Ulva_rigida [6]_strain_U1_MT160686 previously_U._pseudorotundata' -> Ulva_rigida_[6]_strain_U1_MT160686 NOTE: Change sequence name 'Ulva_lacinulata [34]_strain_U2_MT160687 previously_U._laetevirens' -> Ulva_lacinulata_[34]_strain_U2_MT160687 NOTE: Change sequence name 'Ulva_sp.A_AF-2021 [29]_strain_U3_MT160688 previously_U._rigida' -> Ulva_sp.A_AF-2021_[29]_strain_U3_MT160688 NOTE: Change sequence name 'Ulva_lacinulata [4]_strain_U4_MT160689 previously_U._laetevirens' -> Ulva_lacinulata_[4]_strain_U4_MT160689 NOTE: Change sequence name 'Ulva_fenestrata [11]_strain_U17_MT160662' -> Ulva_fenestrata_[11]_strain_U17_MT160662 NOTE: Change sequence name 'Ulva_gigantea [10]_strain_U31_MT160676' -> Ulva_gigantea_[10]_strain_U31_MT160676 NOTE: Change sequence name 'Ulva_australis [3]_strain_U32_MT160679' -> Ulva_australis_[3]_strain_U32_MT160679 NOTE: Change sequence name 'Ulva_australis [13]_strain_U40_MT160695' -> Ulva_australis_[13]_strain_U40_MT160695 NOTE: Change sequence name 'Ulva_armoricana_MNHN [1]_MT078955 HOLOTYPE (reversed)' -> Ulva_armoricana_MNHN_[1]_MT078955 NOTE: Change sequence name 'Ulva_rigida_var_fimbriata_MNHN [1]_MT078957 (reversed)' -> Ulva_rigida_var_fimbriata_MNHN_[1]_MT078957 NOTE: Change sequence name 'Ulva_scandinavica_MNHN [1]_MT078956 (reversed)' -> Ulva_scandinavica_MNHN_[1]_MT078956 NOTE: Change sequence name 'Ulva_arasakii [10]_AB561079' -> Ulva_arasakii_[10]_AB561079 NOTE: Change sequence name 'Ulva_australis [1]_MH538644' -> Ulva_australis_[1]_MH538644 NOTE: Change sequence name 'Ulva_australis [143]_HQ610378' -> Ulva_australis_[143]_HQ610378 NOTE: Change sequence name 'Ulva_beytensis [1]_KC661441' -> Ulva_beytensis_[1]_KC661441 NOTE: Change sequence name 'Ulva_californica [1]_MH538645' -> Ulva_californica_[1]_MH538645 NOTE: Change sequence name 'Ulva_californica [1]_MK992200' -> Ulva_californica_[1]_MK992200 NOTE: Change sequence name 'Ulva_californica [9]_AY454401' -> Ulva_californica_[9]_AY454401 NOTE: Change sequence name 'Ulva_californica [18]_MH538646' -> Ulva_californica_[18]_MH538646 NOTE: Change sequence name 'Ulva_chaugulii [2]_MG976862' -> Ulva_chaugulii_[2]_MG976862 NOTE: Change sequence name 'Ulva_erecta [1]_KC661427' -> Ulva_erecta_[1]_KC661427 NOTE: Change sequence name 'Ulva_expansa [21]_MH731007 HOLOTYPE' -> Ulva_expansa_[21]_MH731007 NOTE: Change sequence name 'Ulva_fasciata [1]_KC661452' -> Ulva_fasciata_[1]_KC661452 NOTE: Change sequence name 'Ulva_fasciata [2]_KC661442' -> Ulva_fasciata_[2]_KC661442 NOTE: Change sequence name 'Ulva_fasciata [2]_MG918119' -> Ulva_fasciata_[2]_MG918119 NOTE: Change sequence name 'Ulva_fasciata [2]_MK125445' -> Ulva_fasciata_[2]_MK125445 NOTE: Change sequence name 'Ulva_fasciata [4]_MG963807' -> Ulva_fasciata_[4]_MG963807 NOTE: Change sequence name 'Ulva_fasciata [24]_JN029299' -> Ulva_fasciata_[24]_JN029299 NOTE: Change sequence name 'Ulva_fenestrata [1]_MK456404 HOLOTYPE' -> Ulva_fenestrata_[1]_MK456404 NOTE: Change sequence name 'Ulva_gigantea [5]_HQ610297' -> Ulva_gigantea_[5]_HQ610297 NOTE: Change sequence name 'Ulva_iliohaha [1]_KT932976 HOLOTYPE' -> Ulva_iliohaha_[1]_KT932976 NOTE: Change sequence name 'Ulva_lactuca [1]_KC661443' -> Ulva_lactuca_[1]_KC661443 NOTE: Change sequence name 'Ulva_lactuca [2]_MH730972 as Ulva_lobata_LECTOTYPE' -> Ulva_lactuca_[2]_MH730972 NOTE: Change sequence name 'Ulva_lactuca [73]_HQ610327' -> Ulva_lactuca_[73]_HQ610327 NOTE: Change sequence name 'Ulva_lactuca [107]_HQ610325' -> Ulva_lactuca_[107]_HQ610325 NOTE: Change sequence name 'Ulva_laetevirens [1]_LT969813' -> Ulva_laetevirens_[1]_LT969813 NOTE: Change sequence name 'Ulva_laetevirens [30]_HQ610428' -> Ulva_laetevirens_[30]_HQ610428 NOTE: Change sequence name 'Ulva_lobata [30]_HQ610369' -> Ulva_lobata_[30]_HQ610369 NOTE: Change sequence name 'Ulva_ohiohilulu [9]_KT932977 HOLOTYPE' -> Ulva_ohiohilulu_[9]_KT932977 NOTE: Change sequence name 'Ulva_ohnoi [107]_AP018696' -> Ulva_ohnoi_[107]_AP018696 NOTE: Change sequence name 'Ulva_pertusa [5]_HE600186' -> Ulva_pertusa_[5]_HE600186 NOTE: Change sequence name 'Ulva_reticulata_x_Ulva_taeniata [3]_KC661468' -> Ulva_reticulata_x_Ulva_taeniata_[3]_KC661468 NOTE: Change sequence name 'Ulva_reticulata [1]_KC661444' -> Ulva_reticulata_[1]_KC661444 NOTE: Change sequence name 'Ulva_reticulata [2]_MG963806' -> Ulva_reticulata_[2]_MG963806 NOTE: Change sequence name 'Ulva_rigida [1]_KC661447' -> Ulva_rigida_[1]_KC661447 NOTE: Change sequence name 'Ulva_rigida [14]_HE600178' -> Ulva_rigida_[14]_HE600178 NOTE: Change sequence name 'Ulva_shanxiensis [1]_KJ617036' -> Ulva_shanxiensis_[1]_KJ617036 NOTE: Change sequence name 'Ulva_shanxiensis [1]_MG918122' -> Ulva_shanxiensis_[1]_MG918122 NOTE: Change sequence name 'Ulva_shanxiensis [1]_MH105040' -> Ulva_shanxiensis_[1]_MH105040 NOTE: Change sequence name 'Ulva_shanxiensis [1]_MH538697' -> Ulva_shanxiensis_[1]_MH538697 NOTE: Change sequence name 'Ulva_shanxiensis [2]_MG918120' -> Ulva_shanxiensis_[2]_MG918120 NOTE: Change sequence name 'Ulva_taeniata [1]_KC661445' -> Ulva_taeniata_[1]_KC661445 NOTE: Change sequence name 'Ulva_taeniata [1]_KC661451' -> Ulva_taeniata_[1]_KC661451 NOTE: Change sequence name 'Ulva_tanneri [1]_KM255002' -> Ulva_tanneri_[1]_KM255002 NOTE: Change sequence name 'Ulva_tepida [8]_KF195538' -> Ulva_tepida_[8]_KF195538 NOTE: Change sequence name 'Umbraulva_japonica [3]_JN029344' -> Umbraulva_japonica_[3]_JN029344 NOTE: Change sequence name 'Ulva_expansa [1]_KM255021' -> Ulva_expansa_[1]_KM255021 NOTE: Change sequence name 'Ulva_fasciata [1]_KC661448' -> Ulva_fasciata_[1]_KC661448 NOTE: Change sequence name 'Ulva_australis [13]_MT894961_strain_BLD1' -> Ulva_australis_[13]_MT894961_strain_BLD1 NOTE: Change sequence name 'Ulva_australis [8]_MT8949778_strain_BUR13' -> Ulva_australis_[8]_MT8949778_strain_BUR13 NOTE: Change sequence name 'Ulva_fenestrata [19]_MT894992_strain_FLY1' -> Ulva_fenestrata_[19]_MT894992_strain_FLY1 NOTE: Change sequence name 'Ulva_fenestrata [1]_MT895033_strain_LOO02' -> Ulva_fenestrata_[1]_MT895033_strain_LOO02 NOTE: Change sequence name 'Ulva_gigantea [2]_MT895017_strain_HUN4' -> Ulva_gigantea_[2]_MT895017_strain_HUN4 NOTE: Change sequence name 'Ulva_gigantea [9]_MT895018_strain_HUN5' -> Ulva_gigantea_[9]_MT895018_strain_HUN5 NOTE: Change sequence name 'Ulva_lacinulata [36]_MT894960 as_U._laetevirens_strain_BELMIXC' -> Ulva_lacinulata_[36]_MT894960 NOTE: Change sequence name 'Ulva_lacinulata [4]_MT895003 as_U._laetevirens_strain_GREEN10' -> Ulva_lacinulata_[4]_MT895003 NOTE: Change sequence name 'Ulva_lacinulata [2]_MT895005 as_U._laetevirens_strain_GREEN26' -> Ulva_lacinulata_[2]_MT895005 NOTE: Change sequence name 'Ulva_lacinulata [2]_MT895013 as_U._laetevirens_strain_HEE38' -> Ulva_lacinulata_[2]_MT895013 NOTE: Change sequence name 'Ulva_ohnoi [3]_MT894982_strain_CORTADURA' -> Ulva_ohnoi_[3]_MT894982_strain_CORTADURA NOTE: Change sequence name 'Ulva_rigida [13]_MT894983 as_U._pseudorotundata_strain_COZ1' -> Ulva_rigida_[13]_MT894983 NOTE: Change sequence name 'Ulva_rigida [1]_MT895104 as_U._pseudorotundata_strain_VEN24' -> Ulva_rigida_[1]_MT895104 NOTE: Change sequence name 'Ulva_sp.A_AF-2021 [4]_MT894990 as_U._rigida_strain_DOG5' -> Ulva_sp.A_AF-2021_[4]_MT894990 NOTE: Change sequence name 'Ulva_sp.A_AF-2021 [1]_MT895102 as_U._rigida_strain_VCO2' -> Ulva_sp.A_AF-2021_[1]_MT895102 NOTE: Change sequence name 'Ulva_lacinulata [1] MW543061 Lesina_voucher_L0054997_LECTOTYPE' -> Ulva_lacinulata_[1] NOTE: Change sequence name 'Ulva_rigida [1]_MW543060 Cadiz_voucher_LD14294_LECTOTYPE' -> Ulva_rigida_[1]_MW543060 NOTE: Change sequence name 'Ulva_rotundata [1]_NC053616_strain_U112_complete_genome' -> Ulva_rotundata_[1]_NC053616_strain_U112_complete_genome Alignment most likely contains DNA/RNA sequences Alignment has 81 sequences with 500 columns, 135 distinct patterns 103 parsimony-informative, 30 singleton sites, 367 constant sites WARNING: Some sequence names are changed as follows: Haplotype_1_[192]_MT078946 -> Haplotype_1__192__MT078946 Haplotype_2_[95]_MT078949 -> Haplotype_2__95__MT078949 Haplotype_3_[9]_MT078951 -> Haplotype_3__9__MT078951 Haplotype_4_[41]_MT078952 -> Haplotype_4__41__MT078952 Haplotype_5_[2]_MT078954 -> Haplotype_5__2__MT078954 Ulva_rigida_[6]_strain_U1_MT160686 -> Ulva_rigida__6__strain_U1_MT160686 Ulva_lacinulata_[34]_strain_U2_MT160687 -> Ulva_lacinulata__34__strain_U2_MT160687 Ulva_sp.A_AF-2021_[29]_strain_U3_MT160688 -> Ulva_sp.A_AF-2021__29__strain_U3_MT160688 Ulva_lacinulata_[4]_strain_U4_MT160689 -> Ulva_lacinulata__4__strain_U4_MT160689 Ulva_fenestrata_[11]_strain_U17_MT160662 -> Ulva_fenestrata__11__strain_U17_MT160662 Ulva_gigantea_[10]_strain_U31_MT160676 -> Ulva_gigantea__10__strain_U31_MT160676 Ulva_australis_[3]_strain_U32_MT160679 -> Ulva_australis__3__strain_U32_MT160679 Ulva_australis_[13]_strain_U40_MT160695 -> Ulva_australis__13__strain_U40_MT160695 Ulva_armoricana_MNHN_[1]_MT078955 -> Ulva_armoricana_MNHN__1__MT078955 Ulva_rigida_var_fimbriata_MNHN_[1]_MT078957 -> Ulva_rigida_var_fimbriata_MNHN__1__MT078957 Ulva_scandinavica_MNHN_[1]_MT078956 -> Ulva_scandinavica_MNHN__1__MT078956 Ulva_arasakii_[10]_AB561079 -> Ulva_arasakii__10__AB561079 Ulva_australis_[1]_MH538644 -> Ulva_australis__1__MH538644 Ulva_australis_[143]_HQ610378 -> Ulva_australis__143__HQ610378 Ulva_beytensis_[1]_KC661441 -> Ulva_beytensis__1__KC661441 Ulva_californica_[1]_MH538645 -> Ulva_californica__1__MH538645 Ulva_californica_[1]_MK992200 -> Ulva_californica__1__MK992200 Ulva_californica_[9]_AY454401 -> Ulva_californica__9__AY454401 Ulva_californica_[18]_MH538646 -> Ulva_californica__18__MH538646 Ulva_chaugulii_[2]_MG976862 -> Ulva_chaugulii__2__MG976862 Ulva_erecta_[1]_KC661427 -> Ulva_erecta__1__KC661427 Ulva_expansa_[21]_MH731007 -> Ulva_expansa__21__MH731007 Ulva_fasciata_[1]_KC661452 -> Ulva_fasciata__1__KC661452 Ulva_fasciata_[2]_KC661442 -> Ulva_fasciata__2__KC661442 Ulva_fasciata_[2]_MG918119 -> Ulva_fasciata__2__MG918119 Ulva_fasciata_[2]_MK125445 -> Ulva_fasciata__2__MK125445 Ulva_fasciata_[4]_MG963807 -> Ulva_fasciata__4__MG963807 Ulva_fasciata_[24]_JN029299 -> Ulva_fasciata__24__JN029299 Ulva_fenestrata_[1]_MK456404 -> Ulva_fenestrata__1__MK456404 Ulva_gigantea_[5]_HQ610297 -> Ulva_gigantea__5__HQ610297 Ulva_iliohaha_[1]_KT932976 -> Ulva_iliohaha__1__KT932976 Ulva_lactuca_[1]_KC661443 -> Ulva_lactuca__1__KC661443 Ulva_lactuca_[2]_MH730972 -> Ulva_lactuca__2__MH730972 Ulva_lactuca_[73]_HQ610327 -> Ulva_lactuca__73__HQ610327 Ulva_lactuca_[107]_HQ610325 -> Ulva_lactuca__107__HQ610325 Ulva_laetevirens_[1]_LT969813 -> Ulva_laetevirens__1__LT969813 Ulva_laetevirens_[30]_HQ610428 -> Ulva_laetevirens__30__HQ610428 Ulva_lobata_[30]_HQ610369 -> Ulva_lobata__30__HQ610369 Ulva_ohiohilulu_[9]_KT932977 -> Ulva_ohiohilulu__9__KT932977 Ulva_ohnoi_[107]_AP018696 -> Ulva_ohnoi__107__AP018696 Ulva_pertusa_[5]_HE600186 -> Ulva_pertusa__5__HE600186 Ulva_reticulata_x_Ulva_taeniata_[3]_KC661468 -> Ulva_reticulata_x_Ulva_taeniata__3__KC661468 Ulva_reticulata_[1]_KC661444 -> Ulva_reticulata__1__KC661444 Ulva_reticulata_[2]_MG963806 -> Ulva_reticulata__2__MG963806 Ulva_rigida_[1]_KC661447 -> Ulva_rigida__1__KC661447 Ulva_rigida_[14]_HE600178 -> Ulva_rigida__14__HE600178 Ulva_shanxiensis_[1]_KJ617036 -> Ulva_shanxiensis__1__KJ617036 Ulva_shanxiensis_[1]_MG918122 -> Ulva_shanxiensis__1__MG918122 Ulva_shanxiensis_[1]_MH105040 -> Ulva_shanxiensis__1__MH105040 Ulva_shanxiensis_[1]_MH538697 -> Ulva_shanxiensis__1__MH538697 Ulva_shanxiensis_[2]_MG918120 -> Ulva_shanxiensis__2__MG918120 Ulva_taeniata_[1]_KC661445 -> Ulva_taeniata__1__KC661445 Ulva_taeniata_[1]_KC661451 -> Ulva_taeniata__1__KC661451 Ulva_tanneri_[1]_KM255002 -> Ulva_tanneri__1__KM255002 Ulva_tepida_[8]_KF195538 -> Ulva_tepida__8__KF195538 Umbraulva_japonica_[3]_JN029344 -> Umbraulva_japonica__3__JN029344 Ulva_expansa_[1]_KM255021 -> Ulva_expansa__1__KM255021 Ulva_fasciata_[1]_KC661448 -> Ulva_fasciata__1__KC661448 Ulva_australis_[13]_MT894961_strain_BLD1 -> Ulva_australis__13__MT894961_strain_BLD1 Ulva_australis_[8]_MT8949778_strain_BUR13 -> Ulva_australis__8__MT8949778_strain_BUR13 Ulva_fenestrata_[19]_MT894992_strain_FLY1 -> Ulva_fenestrata__19__MT894992_strain_FLY1 Ulva_fenestrata_[1]_MT895033_strain_LOO02 -> Ulva_fenestrata__1__MT895033_strain_LOO02 Ulva_gigantea_[2]_MT895017_strain_HUN4 -> Ulva_gigantea__2__MT895017_strain_HUN4 Ulva_gigantea_[9]_MT895018_strain_HUN5 -> Ulva_gigantea__9__MT895018_strain_HUN5 Ulva_lacinulata_[36]_MT894960 -> Ulva_lacinulata__36__MT894960 Ulva_lacinulata_[4]_MT895003 -> Ulva_lacinulata__4__MT895003 Ulva_lacinulata_[2]_MT895005 -> Ulva_lacinulata__2__MT895005 Ulva_lacinulata_[2]_MT895013 -> Ulva_lacinulata__2__MT895013 Ulva_ohnoi_[3]_MT894982_strain_CORTADURA -> Ulva_ohnoi__3__MT894982_strain_CORTADURA Ulva_rigida_[13]_MT894983 -> Ulva_rigida__13__MT894983 Ulva_rigida_[1]_MT895104 -> Ulva_rigida__1__MT895104 Ulva_sp.A_AF-2021_[4]_MT894990 -> Ulva_sp.A_AF-2021__4__MT894990 Ulva_sp.A_AF-2021_[1]_MT895102 -> Ulva_sp.A_AF-2021__1__MT895102 Ulva_lacinulata_[1] -> Ulva_lacinulata__1_ Ulva_rigida_[1]_MW543060 -> Ulva_rigida__1__MW543060 Ulva_rotundata_[1]_NC053616_strain_U112_complete_genome -> Ulva_rotundata__1__NC053616_strain_U112_complete_genome Gap/Ambiguity Composition p-value 1 Haplotype_1__192__MT078946 0.00% passed 99.09% 2 Haplotype_2__95__MT078949 0.00% passed 96.29% 3 Haplotype_3__9__MT078951 0.00% passed 95.36% 4 Haplotype_4__41__MT078952 0.00% passed 99.91% 5 Haplotype_5__2__MT078954 0.00% passed 89.29% 6 Ulva_rigida__6__strain_U1_MT160686 0.00% passed 95.36% 7 Ulva_lacinulata__34__strain_U2_MT160687 0.00% passed 99.09% 8 Ulva_sp.A_AF-2021__29__strain_U3_MT160688 0.00% passed 96.29% 9 Ulva_lacinulata__4__strain_U4_MT160689 0.00% passed 99.44% 10 Ulva_fenestrata__11__strain_U17_MT160662 0.00% passed 89.29% 11 Ulva_gigantea__10__strain_U31_MT160676 0.00% passed 94.39% 12 Ulva_australis__3__strain_U32_MT160679 0.00% passed 99.54% 13 Ulva_australis__13__strain_U40_MT160695 0.00% passed 99.91% 14 Ulva_armoricana_MNHN__1__MT078955 0.00% passed 99.09% 15 Ulva_rigida_var_fimbriata_MNHN__1__MT078957 0.00% passed 99.50% 16 Ulva_scandinavica_MNHN__1__MT078956 0.00% passed 99.09% 17 Ulva_arasakii__10__AB561079 0.20% passed 99.43% 18 Ulva_australis__1__MH538644 0.60% passed 100.00% 19 Ulva_australis__143__HQ610378 0.00% passed 99.91% 20 Ulva_beytensis__1__KC661441 0.00% passed 90.75% 21 Ulva_californica__1__MH538645 0.00% passed 98.86% 22 Ulva_californica__1__MK992200 0.00% passed 96.74% 23 Ulva_californica__9__AY454401 0.00% passed 100.00% 24 Ulva_californica__18__MH538646 0.00% passed 99.32% 25 Ulva_chaugulii__2__MG976862 0.00% passed 99.83% 26 Ulva_erecta__1__KC661427 0.00% passed 97.59% 27 Ulva_expansa__21__MH731007 0.00% passed 99.20% 28 Ulva_fasciata__1__KC661452 0.00% passed 90.75% 29 Ulva_fasciata__2__KC661442 0.00% passed 98.10% 30 Ulva_fasciata__2__MG918119 0.00% passed 97.82% 31 Ulva_fasciata__2__MK125445 0.00% passed 96.06% 32 Ulva_fasciata__4__MG963807 0.00% passed 95.30% 33 Ulva_fasciata__24__JN029299 0.00% passed 98.35% 34 Ulva_fenestrata__1__MK456404 0.00% passed 84.45% 35 Ulva_gigantea__5__HQ610297 0.00% passed 94.39% 36 Ulva_iliohaha__1__KT932976 0.00% passed 99.61% 37 Ulva_lactuca__1__KC661443 0.00% passed 99.86% 38 Ulva_lactuca__2__MH730972 0.00% passed 98.35% 39 Ulva_lactuca__73__HQ610327 0.00% passed 84.45% 40 Ulva_lactuca__107__HQ610325 0.00% passed 89.29% 41 Ulva_laetevirens__1__LT969813 0.00% passed 99.58% 42 Ulva_laetevirens__30__HQ610428 0.00% passed 99.44% 43 Ulva_lobata__30__HQ610369 0.00% passed 99.20% 44 Ulva_ohiohilulu__9__KT932977 0.00% passed 73.92% 45 Ulva_ohnoi__107__AP018696 0.00% passed 95.30% 46 Ulva_pertusa__5__HE600186 0.00% passed 99.91% 47 Ulva_reticulata_x_Ulva_taeniata__3__KC661468 0.00% passed 98.35% 48 Ulva_reticulata__1__KC661444 0.00% passed 98.86% 49 Ulva_reticulata__2__MG963806 0.00% passed 98.35% 50 Ulva_rigida__1__KC661447 0.00% passed 99.44% 51 Ulva_rigida__14__HE600178 0.00% passed 99.44% 52 Ulva_shanxiensis__1__KJ617036 0.00% passed 97.23% 53 Ulva_shanxiensis__1__MG918122 0.00% passed 95.94% 54 Ulva_shanxiensis__1__MH105040 0.00% passed 90.95% 55 Ulva_shanxiensis__1__MH538697 0.40% passed 95.97% 56 Ulva_shanxiensis__2__MG918120 0.00% passed 93.91% 57 Ulva_taeniata__1__KC661445 0.00% passed 97.82% 58 Ulva_taeniata__1__KC661451 0.00% passed 90.75% 59 Ulva_tanneri__1__KM255002 0.00% passed 98.66% 60 Ulva_tepida__8__KF195538 0.00% passed 96.52% 61 Umbraulva_japonica__3__JN029344 0.00% passed 98.12% 62 Ulva_expansa__1__KM255021 0.00% passed 99.99% 63 Ulva_fasciata__1__KC661448 0.00% passed 94.49% 64 Ulva_australis__13__MT894961_strain_BLD1 0.00% passed 99.91% 65 Ulva_australis__8__MT8949778_strain_BUR13 0.00% passed 99.54% 66 Ulva_fenestrata__19__MT894992_strain_FLY1 0.00% passed 89.29% 67 Ulva_fenestrata__1__MT895033_strain_LOO02 0.00% passed 89.29% 68 Ulva_gigantea__2__MT895017_strain_HUN4 0.00% passed 94.39% 69 Ulva_gigantea__9__MT895018_strain_HUN5 0.00% passed 94.39% 70 Ulva_lacinulata__36__MT894960 0.00% passed 99.09% 71 Ulva_lacinulata__4__MT895003 0.00% passed 99.44% 72 Ulva_lacinulata__2__MT895005 0.00% passed 99.44% 73 Ulva_lacinulata__2__MT895013 0.00% passed 99.09% 74 Ulva_ohnoi__3__MT894982_strain_CORTADURA 0.00% passed 95.30% 75 Ulva_rigida__13__MT894983 0.00% passed 95.36% 76 Ulva_rigida__1__MT895104 0.00% passed 95.36% 77 Ulva_sp.A_AF-2021__4__MT894990 0.00% passed 96.29% 78 Ulva_sp.A_AF-2021__1__MT895102 0.00% passed 96.29% 79 Ulva_lacinulata__1_ 0.00% passed 99.44% 80 Ulva_rigida__1__MW543060 0.00% passed 95.36% 81 Ulva_rotundata__1__NC053616_strain_U112_complete_genome 0.00% passed 95.36% **** TOTAL 0.01% 0 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: Ulva_lacinulata__34__strain_U2_MT160687 is identical to Haplotype_1__192__MT078946 but kept for subsequent analysis NOTE: Ulva_sp.A_AF-2021__29__strain_U3_MT160688 is identical to Haplotype_2__95__MT078949 but kept for subsequent analysis NOTE: Ulva_rigida__6__strain_U1_MT160686 is identical to Haplotype_3__9__MT078951 but kept for subsequent analysis NOTE: Ulva_australis__13__strain_U40_MT160695 is identical to Haplotype_4__41__MT078952 but kept for subsequent analysis NOTE: Ulva_fenestrata__11__strain_U17_MT160662 is identical to Haplotype_5__2__MT078954 but kept for subsequent analysis NOTE: Ulva_laetevirens__30__HQ610428 is identical to Ulva_lacinulata__4__strain_U4_MT160689 but kept for subsequent analysis NOTE: Ulva_gigantea__5__HQ610297 is identical to Ulva_gigantea__10__strain_U31_MT160676 but kept for subsequent analysis NOTE: Ulva_australis__8__MT8949778_strain_BUR13 is identical to Ulva_australis__3__strain_U32_MT160679 but kept for subsequent analysis NOTE: Ulva_fasciata__1__KC661452 is identical to Ulva_beytensis__1__KC661441 but kept for subsequent analysis NOTE: Ulva_lobata__30__HQ610369 is identical to Ulva_expansa__21__MH731007 but kept for subsequent analysis NOTE: Ulva_ohnoi__107__AP018696 is identical to Ulva_fasciata__4__MG963807 but kept for subsequent analysis NOTE: Ulva_lactuca__2__MH730972 is identical to Ulva_fasciata__24__JN029299 but kept for subsequent analysis NOTE: 26 identical sequences (see below) will be ignored for subsequent analysis NOTE: Ulva_armoricana_MNHN__1__MT078955 (identical to Haplotype_1__192__MT078946) is ignored but added at the end NOTE: Ulva_scandinavica_MNHN__1__MT078956 (identical to Haplotype_1__192__MT078946) is ignored but added at the end NOTE: Ulva_lacinulata__36__MT894960 (identical to Haplotype_1__192__MT078946) is ignored but added at the end NOTE: Ulva_lacinulata__2__MT895013 (identical to Haplotype_1__192__MT078946) is ignored but added at the end NOTE: Ulva_sp.A_AF-2021__4__MT894990 (identical to Haplotype_2__95__MT078949) is ignored but added at the end NOTE: Ulva_sp.A_AF-2021__1__MT895102 (identical to Haplotype_2__95__MT078949) is ignored but added at the end NOTE: Ulva_rigida__13__MT894983 (identical to Haplotype_3__9__MT078951) is ignored but added at the end NOTE: Ulva_rigida__1__MT895104 (identical to Haplotype_3__9__MT078951) is ignored but added at the end NOTE: Ulva_rigida__1__MW543060 (identical to Haplotype_3__9__MT078951) is ignored but added at the end NOTE: Ulva_rotundata__1__NC053616_strain_U112_complete_genome (identical to Haplotype_3__9__MT078951) is ignored but added at the end NOTE: Ulva_australis__143__HQ610378 (identical to Haplotype_4__41__MT078952) is ignored but added at the end NOTE: Ulva_pertusa__5__HE600186 (identical to Haplotype_4__41__MT078952) is ignored but added at the end NOTE: Ulva_australis__13__MT894961_strain_BLD1 (identical to Haplotype_4__41__MT078952) is ignored but added at the end NOTE: Ulva_lactuca__107__HQ610325 (identical to Haplotype_5__2__MT078954) is ignored but added at the end NOTE: Ulva_fenestrata__19__MT894992_strain_FLY1 (identical to Haplotype_5__2__MT078954) is ignored but added at the end NOTE: Ulva_fenestrata__1__MT895033_strain_LOO02 (identical to Haplotype_5__2__MT078954) is ignored but added at the end NOTE: Ulva_rigida__14__HE600178 (identical to Ulva_lacinulata__4__strain_U4_MT160689) is ignored but added at the end NOTE: Ulva_lacinulata__4__MT895003 (identical to Ulva_lacinulata__4__strain_U4_MT160689) is ignored but added at the end NOTE: Ulva_lacinulata__2__MT895005 (identical to Ulva_lacinulata__4__strain_U4_MT160689) is ignored but added at the end NOTE: Ulva_lacinulata__1_ (identical to Ulva_lacinulata__4__strain_U4_MT160689) is ignored but added at the end NOTE: Ulva_gigantea__2__MT895017_strain_HUN4 (identical to Ulva_gigantea__10__strain_U31_MT160676) is ignored but added at the end NOTE: Ulva_gigantea__9__MT895018_strain_HUN5 (identical to Ulva_gigantea__10__strain_U31_MT160676) is ignored but added at the end NOTE: Ulva_taeniata__1__KC661451 (identical to Ulva_beytensis__1__KC661441) is ignored but added at the end NOTE: Ulva_ohnoi__3__MT894982_strain_CORTADURA (identical to Ulva_fasciata__4__MG963807) is ignored but added at the end NOTE: Ulva_reticulata_x_Ulva_taeniata__3__KC661468 (identical to Ulva_fasciata__24__JN029299) is ignored but added at the end NOTE: Ulva_reticulata__2__MG963806 (identical to Ulva_fasciata__24__JN029299) is ignored but added at the end For your convenience alignment with unique sequences printed to /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.uniqueseq.phy Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.002 seconds NOTE: ModelFinder requires 3 MB RAM! ModelFinder will test 286 DNA models (sample size: 500) ... No. Model -LnL df AIC AICc BIC Measuring multi-threading efficiency up to 8 CPU cores Increase to 10 rounds for branch lengths 1839 trees examined Threads: 1 / Time: 8.004 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -5972 Threads: 2 / Time: 7.649 sec / Speedup: 1.046 / Efficiency: 52% / LogL: -5972 Threads: 3 / Time: 9.386 sec / Speedup: 0.853 / Efficiency: 28% / LogL: -5972 BEST NUMBER OF THREADS: 1 1 JC 2696.681 107 5607.362 5666.321 6058.325 2 JC+I 2537.360 108 5290.719 5350.934 5745.897 3 JC+G4 2530.676 108 5277.352 5337.567 5732.530 4 JC+I+G4 2522.033 109 5262.066 5323.553 5721.458 5 JC+R2 2531.305 109 5280.611 5342.098 5740.003 6 JC+R3 2529.468 111 5280.936 5345.018 5748.757 14 F81+F 2686.295 110 5592.591 5655.367 6056.198 15 F81+F+I 2521.777 111 5265.553 5329.636 5733.375 16 F81+F+G4 2515.785 111 5253.570 5317.653 5721.392 17 F81+F+I+G4 2507.037 112 5238.073 5303.479 5710.110 18 F81+F+R2 2515.735 112 5255.471 5320.876 5727.507 19 F81+F+R3 2514.787 114 5257.574 5325.678 5738.040 27 K2P 2656.471 108 5528.941 5589.156 5984.119 28 K2P+I 2495.152 109 5208.304 5269.791 5667.696 29 K2P+G4 2488.181 109 5194.363 5255.850 5653.755 30 K2P+I+G4 2478.603 110 5177.206 5239.983 5640.813 31 K2P+R2 2486.695 110 5193.390 5256.166 5656.996 32 K2P+R3 2486.146 112 5196.292 5261.698 5668.328 40 HKY+F 2639.940 111 5501.880 5565.963 5969.702 41 HKY+F+I 2470.035 112 5164.069 5229.475 5636.105 42 HKY+F+G4 2463.420 112 5150.841 5216.246 5622.877 43 HKY+F+I+G4 2453.918 113 5133.836 5200.582 5610.087 44 HKY+F+R2 2462.969 113 5151.939 5218.685 5628.189 45 HKY+F+R3 2462.714 115 5155.428 5224.907 5640.108 53 TNe 2656.023 109 5530.047 5591.534 5989.439 54 TNe+I 2495.097 110 5210.194 5272.970 5673.801 55 TNe+G4 2488.016 110 5196.031 5258.808 5659.638 56 TNe+I+G4 2478.199 111 5178.398 5242.480 5646.219 57 TNe+R2 2486.122 111 5194.245 5258.327 5662.066 58 TNe+R3 2485.831 113 5197.662 5264.408 5673.913 66 TN+F 2639.013 112 5502.025 5567.431 5974.061 67 TN+F+I 2468.033 113 5162.067 5228.813 5638.317 68 TN+F+G4 2461.768 113 5149.536 5216.282 5625.787 69 TN+F+I+G4 2451.629 114 5131.258 5199.362 5611.723 70 TN+F+R2 2461.383 114 5150.767 5218.871 5631.232 71 TN+F+R3 2461.134 116 5154.267 5225.139 5643.162 79 K3P 2656.469 109 5530.938 5592.425 5990.330 80 K3P+I 2495.159 110 5210.317 5273.094 5673.924 81 K3P+G4 2488.188 110 5196.375 5259.152 5659.982 82 K3P+I+G4 2478.194 111 5178.389 5242.471 5646.210 83 K3P+R2 2486.320 111 5194.641 5258.723 5662.462 84 K3P+R3 2486.018 113 5198.036 5264.783 5674.287 92 K3Pu+F 2639.396 112 5502.792 5568.198 5974.828 93 K3Pu+F+I 2468.374 113 5162.749 5229.495 5639.000 94 K3Pu+F+G4 2461.764 113 5149.529 5216.275 5625.779 95 K3Pu+F+I+G4 2451.821 114 5131.643 5199.747 5612.108 96 K3Pu+F+R2 2461.283 114 5150.566 5218.670 5631.031 97 K3Pu+F+R3 2461.063 116 5154.127 5224.999 5643.021 105 TPM2+F 2639.947 112 5503.893 5569.299 5975.930 106 TPM2+F+I 2469.475 113 5164.950 5231.696 5641.200 107 TPM2+F+G4 2462.734 113 5151.467 5218.213 5627.718 108 TPM2+F+I+G4 2452.898 114 5133.795 5201.899 5614.260 109 TPM2+F+R2 2462.182 114 5152.365 5220.469 5632.830 110 TPM2+F+R3 2461.979 116 5155.959 5226.831 5644.853 118 TPM2u+F 2639.948 112 5503.895 5569.301 5975.931 119 TPM2u+F+I 2469.476 113 5164.952 5231.698 5641.202 120 TPM2u+F+G4 2462.735 113 5151.469 5218.215 5627.720 121 TPM2u+F+I+G4 2452.864 114 5133.727 5201.831 5614.193 122 TPM2u+F+R2 2462.134 114 5152.268 5220.372 5632.734 123 TPM2u+F+R3 2461.930 116 5155.859 5226.731 5644.754 131 TPM3+F 2632.300 112 5488.600 5554.005 5960.636 132 TPM3+F+I 2458.925 113 5143.849 5210.596 5620.100 133 TPM3+F+G4 2451.548 113 5129.096 5195.842 5605.346 134 TPM3+F+I+G4 2440.473 114 5108.947 5177.051 5589.412 135 TPM3+F+R2 2451.623 114 5131.247 5199.351 5611.712 136 TPM3+F+R3 2451.199 116 5134.398 5205.270 5623.292 144 TPM3u+F 2632.301 112 5488.602 5554.008 5960.638 145 TPM3u+F+I 2458.924 113 5143.848 5210.594 5620.098 146 TPM3u+F+G4 2451.548 113 5129.097 5195.843 5605.347 147 TPM3u+F+I+G4 2440.467 114 5108.934 5177.037 5589.399 148 TPM3u+F+R2 2451.610 114 5131.219 5199.323 5611.685 149 TPM3u+F+R3 2451.102 116 5134.204 5205.076 5623.099 157 TIMe 2656.021 110 5532.042 5594.818 5995.649 158 TIMe+I 2495.102 111 5212.204 5276.287 5680.026 159 TIMe+G4 2488.021 111 5198.042 5262.124 5665.863 160 TIMe+I+G4 2477.992 112 5179.985 5245.391 5652.021 161 TIMe+R2 2486.084 112 5196.168 5261.574 5668.204 162 TIMe+R3 2472.554 114 5173.108 5241.212 5653.574 163 TIMe+R4 2472.557 116 5177.114 5247.986 5666.008 170 TIM+F 2638.476 113 5502.952 5569.698 5979.203 171 TIM+F+I 2466.391 114 5160.781 5228.885 5641.247 172 TIM+F+G4 2460.131 114 5148.262 5216.366 5628.728 173 TIM+F+I+G4 2449.613 115 5129.227 5198.706 5613.907 174 TIM+F+R2 2459.741 115 5149.483 5218.962 5634.163 175 TIM+F+R3 2444.696 117 5123.392 5195.675 5616.502 176 TIM+F+R4 2444.682 119 5127.365 5202.523 5628.903 183 TIM2e 2655.023 110 5530.047 5592.823 5993.654 184 TIM2e+I 2494.993 111 5211.985 5276.068 5679.807 185 TIM2e+G4 2487.742 111 5197.485 5261.567 5665.306 186 TIM2e+I+G4 2477.611 112 5179.222 5244.628 5651.258 187 TIM2e+R2 2485.730 112 5195.460 5260.866 5667.497 188 TIM2e+R3 2471.913 114 5171.825 5239.929 5652.290 189 TIM2e+R4 2471.884 116 5175.768 5246.640 5664.663 196 TIM2+F 2639.007 113 5504.015 5570.761 5980.265 197 TIM2+F+I 2467.447 114 5162.893 5230.997 5643.359 198 TIM2+F+G4 2461.055 114 5150.109 5218.213 5630.574 199 TIM2+F+I+G4 2450.676 115 5131.352 5200.831 5616.032 200 TIM2+F+R2 2460.677 115 5151.354 5220.833 5636.034 201 TIM2+F+R3 2445.511 117 5125.023 5197.305 5618.132 202 TIM2+F+R4 2445.468 119 5128.936 5204.094 5630.475 209 TIM3e 2655.246 110 5530.491 5593.268 5994.098 210 TIM3e+I 2494.058 111 5210.115 5274.198 5677.937 211 TIM3e+G4 2487.020 111 5196.039 5260.122 5663.861 212 TIM3e+I+G4 2476.976 112 5177.953 5243.358 5649.989 213 TIM3e+R2 2485.155 112 5194.311 5259.716 5666.347 214 TIM3e+R3 2471.287 114 5170.575 5238.679 5651.040 215 TIM3e+R4 2471.279 116 5174.559 5245.431 5663.453 222 TIM3+F 2631.335 113 5488.670 5555.416 5964.921 223 TIM3+F+I 2456.985 114 5141.971 5210.075 5622.436 224 TIM3+F+G4 2449.672 114 5127.344 5195.448 5607.809 225 TIM3+F+I+G4 2437.933 115 5105.865 5175.344 5590.545 226 TIM3+F+R2 2450.049 115 5130.098 5199.577 5614.778 227 TIM3+F+R3 2432.609 117 5099.217 5171.500 5592.326 228 TIM3+F+R4 2432.607 119 5103.215 5178.373 5604.753 235 TVMe 2654.735 111 5531.470 5595.553 5999.292 236 TVMe+I 2493.993 112 5211.986 5277.392 5684.022 237 TVMe+G4 2487.006 112 5198.013 5263.418 5670.049 238 TVMe+I+G4 2476.818 113 5179.636 5246.382 5655.887 239 TVMe+R2 2485.138 113 5196.276 5263.022 5672.527 240 TVMe+R3 2470.520 115 5171.040 5240.519 5655.720 241 TVMe+R4 2470.483 117 5174.967 5247.249 5668.076 248 TVM+F 2632.291 114 5492.582 5560.686 5973.048 249 TVM+F+I 2458.285 115 5146.571 5216.050 5631.251 250 TVM+F+G4 2450.750 115 5131.500 5200.979 5616.180 251 TVM+F+I+G4 2439.800 116 5111.599 5182.471 5600.494 252 TVM+F+R2 2451.105 116 5134.211 5205.083 5623.105 253 TVM+F+R3 2434.345 118 5104.690 5178.402 5602.014 254 TVM+F+R4 2434.326 120 5108.652 5185.275 5614.405 261 SYM 2654.283 112 5532.566 5597.971 6004.602 262 SYM+I 2493.923 113 5213.845 5280.591 5690.096 263 SYM+G4 2486.749 113 5199.499 5266.245 5675.749 264 SYM+I+G4 2476.606 114 5181.213 5249.317 5661.678 265 SYM+R2 2484.822 114 5197.644 5265.748 5678.109 266 SYM+R3 2470.421 116 5172.841 5243.713 5661.736 267 SYM+R4 2470.385 118 5176.770 5250.482 5674.094 274 GTR+F 2631.341 115 5492.682 5562.161 5977.362 275 GTR+F+I 2456.337 116 5144.674 5215.546 5633.569 276 GTR+F+G4 2448.855 116 5129.710 5200.582 5618.605 277 GTR+F+I+G4 2437.224 117 5108.447 5180.730 5601.557 278 GTR+F+R2 2449.458 117 5132.917 5205.199 5626.026 279 GTR+F+R3 2431.946 119 5101.892 5177.050 5603.431 280 GTR+F+R4 2431.946 121 5105.892 5183.998 5615.860 Akaike Information Criterion: TIM3+F+R3 Corrected Akaike Information Criterion: TIM3+F+R3 Bayesian Information Criterion: TPM3u+F+I+G4 Best-fit model: TPM3u+F+I+G4 chosen according to BIC All model information printed to /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.model.gz CPU time for ModelFinder: 54.217 seconds (0h:0m:54s) Wall-clock time for ModelFinder: 27.670 seconds (0h:0m:27s) Generating 1000 samples for ultrafast bootstrap (seed: 244917)... NOTE: 1 MB RAM (0 GB) is required! Measuring multi-threading efficiency up to 8 CPU cores Increase to 10 rounds for branch lengths 703 trees examined Threads: 1 / Time: 8.007 sec / Speedup: 1.000 / Efficiency: 100% / LogL: -4478 Threads: 2 / Time: 6.763 sec / Speedup: 1.184 / Efficiency: 59% / LogL: -4478 Threads: 3 / Time: 6.561 sec / Speedup: 1.220 / Efficiency: 41% / LogL: -4478 BEST NUMBER OF THREADS: 2 Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.171 / LogL: -2451.549 Init pinv, alpha: 0.082, 1.000 / Estimate: 0.090, 0.201 / LogL: -2449.910 Init pinv, alpha: 0.163, 1.000 / Estimate: 0.180, 0.241 / LogL: -2448.247 Init pinv, alpha: 0.245, 1.000 / Estimate: 0.552, 0.738 / LogL: -2440.971 Init pinv, alpha: 0.326, 1.000 / Estimate: 0.556, 0.752 / LogL: -2440.918 Init pinv, alpha: 0.408, 1.000 / Estimate: 0.556, 0.753 / LogL: -2440.921 Init pinv, alpha: 0.489, 1.000 / Estimate: 0.554, 0.747 / LogL: -2440.947 Init pinv, alpha: 0.571, 1.000 / Estimate: 0.581, 0.866 / LogL: -2440.616 Init pinv, alpha: 0.652, 1.000 / Estimate: 0.636, 1.284 / LogL: -2440.518 Init pinv, alpha: 0.734, 1.000 / Estimate: 0.636, 1.280 / LogL: -2440.532 Optimal pinv,alpha: 0.636, 1.284 / LogL: -2440.518 Parameters optimization took 0.454 sec Computing ML distances based on estimated model parameters... 0.013 sec Computing BIONJ tree... 0.002 seconds Log-likelihood of BIONJ tree: -2437.491 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.215 second Computing log-likelihood of 98 initial trees ... 0.280 seconds Current best score: -2423.279 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -2422.935 Iteration 10 / LogL: -2425.961 / Time: 0h:0m:22s Iteration 20 / LogL: -2430.363 / Time: 0h:0m:22s Finish initializing candidate tree set (9) Current best tree score: -2422.935 / CPU time: 1.189 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- UPDATE BEST LOG-LIKELIHOOD: -2422.934 Iteration 30 / LogL: -2428.790 / Time: 0h:0m:23s (0h:0m:57s left) Iteration 40 / LogL: -2423.506 / Time: 0h:0m:24s (0h:0m:37s left) UPDATE BEST LOG-LIKELIHOOD: -2422.932 BETTER TREE FOUND at iteration 48: -2422.930 Iteration 50 / LogL: -2423.251 / Time: 0h:0m:24s (0h:0m:49s left) Log-likelihood cutoff on original alignment: -2443.964 Iteration 60 / LogL: -2426.144 / Time: 0h:0m:25s (0h:0m:37s left) UPDATE BEST LOG-LIKELIHOOD: -2422.930 Iteration 70 / LogL: -2422.933 / Time: 0h:0m:25s (0h:0m:29s left) UPDATE BEST LOG-LIKELIHOOD: -2422.929 Iteration 80 / LogL: -2423.505 / Time: 0h:0m:26s (0h:0m:22s left) Iteration 90 / LogL: -2423.370 / Time: 0h:0m:27s (0h:0m:17s left) UPDATE BEST LOG-LIKELIHOOD: -2422.928 Iteration 100 / LogL: -2422.928 / Time: 0h:0m:27s (0h:0m:13s left) Log-likelihood cutoff on original alignment: -2443.964 NOTE: Bootstrap correlation coefficient of split occurrence frequencies: 0.998 UPDATE BEST LOG-LIKELIHOOD: -2422.928 Iteration 110 / LogL: -2422.930 / Time: 0h:0m:28s (0h:0m:23s left) UPDATE BEST LOG-LIKELIHOOD: -2422.927 Iteration 120 / LogL: -2422.931 / Time: 0h:0m:28s (0h:0m:19s left) Iteration 130 / LogL: -2439.286 / Time: 0h:0m:29s (0h:0m:15s left) Iteration 140 / LogL: -2422.928 / Time: 0h:0m:29s (0h:0m:12s left) UPDATE BEST LOG-LIKELIHOOD: -2422.927 TREE SEARCH COMPLETED AFTER 149 ITERATIONS / Time: 0h:0m:30s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -2422.927 2. Current log-likelihood: -2422.915 Optimal log-likelihood: -2422.906 Rate parameters: A-C: 3.18276 A-G: 5.64851 A-T: 1.00000 C-G: 3.18276 C-T: 5.64851 G-T: 1.00000 Base frequencies: A: 0.357 C: 0.136 G: 0.207 T: 0.300 Proportion of invariable sites: 0.628 Gamma shape alpha: 1.277 Parameters optimization took 2 rounds (0.006 sec) BEST SCORE FOUND : -2422.906 Creating bootstrap support values... Split supports printed to NEXUS file /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.splits.nex Total tree length: 0.811 Total number of iterations: 149 CPU time used for tree search: 17.059 sec (0h:0m:17s) Wall-clock time used for tree search: 8.716 sec (0h:0m:8s) Total CPU time used: 59.175 sec (0h:0m:59s) Total wall-clock time used: 30.697 sec (0h:0m:30s) Computing bootstrap consensus tree... Reading input file /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.splits.nex... 55 taxa and 387 splits. Consensus tree written to /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.contree Reading input trees file /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.contree Log-likelihood of consensus tree: -2423.180 Analysis results written to: IQ-TREE report: /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.iqtree Maximum-likelihood tree: /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.treefile Likelihood distances: /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.mldist Ultrafast bootstrap approximation results written to: Split support values: /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.splits.nex Consensus tree: /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.contree Screen log file: /Users/epante/Desktop/Dartois-etal_PeerJ_revised6/REVISED_peerj-52855-Supplemental_S7_Alignment_81seq_500pb_tufA.fasta.log Date and Time: Wed Sep 1 09:55:46 2021