IQ-TREE 1.6.10 built Feb 19 2019 Partition file name: parti.nex.best_scheme Input file name: concatenated_samples.nex Type of analysis: ModelFinder + tree reconstruction + ultrafast bootstrap (10000 replicates) Random seed number: 129219 REFERENCES ---------- To cite ModelFinder please use: Subha Kalyaanamoorthy, Bui Quang Minh, Thomas KF Wong, Arndt von Haeseler, and Lars S Jermiin (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods, 14:587–589. https://doi.org/10.1038/nmeth.4285 To cite IQ-TREE please use: Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol Biol Evol, 32:268-274. https://doi.org/10.1093/molbev/msu300 Since you used ultrafast bootstrap (UFBoot) please also cite: Diep Thi Hoang, Olga Chernomor, Arndt von Haeseler, Bui Quang Minh, and Le Sy Vinh (2017) UFBoot2: Improving the ultrafast bootstrap approximation. Mol Biol Evol, in press. https://doi.org/10.1093/molbev/msx281 Since you used partition models please also cite: Olga Chernomor, Arndt von Haeseler, and Bui Quang Minh (2016) Terrace aware data structure for phylogenomic inference from supermatrices. Syst Biol, 65:997-1008. https://doi.org/10.1093/sysbio/syw037 SEQUENCE ALIGNMENT ------------------ Input data: 11 taxa with 2 partitions and 2749 total sites (0% missing data) ID Name Type Seq Site Unique Infor Invar Const 1 genome_F1_genome_WG DNA 9 1777 62 19 1714 1714 2 genome_F2_genome_LWRh DNA 9 972 13 6 960 960 Column meanings: Unique: Number of unique site patterns Infor: Number of parsimony-informative sites Invar: Number of invariant sites Const: Number of constant sites (can be subset of invariant sites) SUBSTITUTION PROCESS -------------------- Edge-linked-proportional partition model but separate models between partitions ID Model Speed Parameters 1 GTR+F 1.3270 GTR{1.10429,6.27172,0.357969,1.43037,9.53914}+F{0.24518,0.265628,0.282789,0.206402} 2 GTR+F 0.4023 GTR{0.0001,99.9996,0.0001,22.3537,22.1456}+F{0.237083,0.243141,0.248743,0.271033} MAXIMUM LIKELIHOOD TREE ----------------------- Log-likelihood of the tree: -4341.4144 (s.e. 56.8247) Unconstrained log-likelihood (without tree): -5708.4808 Number of free parameters (#branches + #model parameters): 32 Akaike information criterion (AIC) score: 8746.8287 Corrected Akaike information criterion (AICc) score: 8747.6063 Bayesian information criterion (BIC) score: 8936.2365 Total tree length (sum of branch lengths): 0.0310 Sum of internal branch lengths: 0.0090 (28.9200% of tree length) WARNING: 3 near-zero internal branches (<0.0004) should be treated with caution Such branches are denoted by '**' in the figure below NOTE: Tree is UNROOTED although outgroup taxon 'Myc_tur_571_CR071225_02' is drawn at root Numbers in parentheses are ultrafast bootstrap support (%) +**Myc_nsp_312_UGM951118_02 +-------------------| (99) | | +-----Myc_nsp_449_RMMA050801_08 | | +--| (65) | | | +---Myc_nsp_450_RMMA050727_06 | +**| (40) | | +**Myc_nsp_575_JSC030826_01 | +**| (53) | +**Myc_nsp_858_RMMA090930_09 +-----------------------------| (100) | | +--------Myc_zet_451_RMMA050816_04 | +**| (50) | +----------------------Myc_zet_A444_RMMA050818_05 | +----------------------------------Myc_tur_571_CR071225_02 | +-------------------------------------------------------Myc_tur_T25_CR051012_01 Tree in newick format: (((Myc_nsp_312_UGM951118_02:0.0000024274,((Myc_nsp_449_RMMA050801_08:0.0010937440,Myc_nsp_450_RMMA050727_06:0.0007291940)65:0.0003640018,(Myc_nsp_575_JSC030826_01:0.0000024274,Myc_nsp_858_RMMA090930_09:0.0000024274)53:0.0000021131)40:0.0000024274)99:0.0033443622,(Myc_zet_451_RMMA050816_04:0.0015019096,Myc_zet_A444_RMMA050818_05:0.0037318583)50:0.0003393016)100:0.0049142092,(Myc_tur_571_CR071225_02:0.0057391723,Myc_tur_T25_CR051012_01:0.0092272767); CONSENSUS TREE -------------- Consensus tree is constructed from 10000bootstrap trees Log-likelihood of consensus tree: -4341.415120 Robinson-Foulds distance between ML tree and consensus tree: 0 Branches with support >0.000000% are kept (extended consensus) Branch lengths are optimized by maximum likelihood on original alignment Numbers in parentheses are bootstrap supports (%) +--Myc_nsp_312_UGM951118_02 +-------------------| (99) | | +-----Myc_nsp_449_RMMA050801_08 | | +--| (65) | | | +---Myc_nsp_450_RMMA050727_06 | +--| (40) | | +**Myc_nsp_575_JSC030826_01 | | +**| | | | +**Tzet1.0 | | +--| | | | +**Myc_nsp_862_RMMA050105_29 | +--| (53) | +--Myc_nsp_858_RMMA090930_09 +-----------------------------| (100) | | +--------Myc_zet_451_RMMA050816_04 | +--| (50) | +----------------------Myc_zet_A444_RMMA050818_05 | +----------------------------------Myc_tur_571_CR071225_02 | +-------------------------------------------------------Myc_tur_T25_CR051012_01 Consensus tree in newick format: (((Myc_nsp_312_UGM951118_02:0.0000024198,((Myc_nsp_449_RMMA050801_08:0.0010924423,Myc_nsp_450_RMMA050727_06:0.0007284392)65:0.0003644618,(((Myc_nsp_575_JSC030826_01:0.0000000000,Tzet1.0:0.0000000000):0.0000000000,Myc_nsp_862_RMMA050105_29:0.0000000000):0.0000024198,Myc_nsp_858_RMMA090930_09:0.0000024198)53:0.0000024198)40:0.0000024198)99:0.0033447339,(Myc_zet_451_RMMA050816_04:0.0015019936,Myc_zet_A444_RMMA050818_05:0.0037318388)50:0.0003393159)100:0.0049142093,Myc_tur_571_CR071225_02:0.0057391844,Myc_tur_T25_CR051012_01:0.0092273626); TIME STAMP ---------- Date and time: Tue Oct 08 10:29:59 2019 Total CPU time used: 5.96875 seconds (0h:0m:5s) Total wall-clock time used: 6.4322625 seconds (0h:0m:6s)