Command: iqtree-2.2.2.6-MacOSX/bin/iqtree2 --alisim simulated_MSA_enforced_LBA_but_half -t  /L_protein_gblocks_aa_from_nt_constrain_noLBA_but_half_length.treefile -m LG + F + I {0.0464535} + R4 0.300753 0.167457 0.393935 0.678518 0.220204 2.03523 0.0386547 6.05824 --length 1765 --num-alignments 100

Constraint treefile 1 with presumptive LBA involving TAPV and XILV (i.e., a control using the observed topology) is:

(NC_076735Oberlandvirus:0.7923549835,(NC_055176Wenlingthamnaconusseptentrionalis:0.2892724155,(NC_076734_Fiwi_virus:0.1507850772,NC_076916_Kander_virus:0.1313654257):0.2550050514):0.4355959441[&model=LG+F{0.056/0.058/0.033/0.053/0.029/0.030/0.058/0.066/0.036/0.046/0.116/0.045/0.027/0.043/0.048/0.083/0.059/0.012/0.030/0.073}],((NC_076535_Tapajosvirus:0.9785097041[&model=LG+F{0.065/0.059/0.042/0.034/0.027/0.042/0.051/0.052/0.027/0.067/0.122/0.041/0.022/0.046/0.044/0.079/0.066/0.017/0.047/0.054}],NC_055175Wenlingfrogfishfilovirus:1.1453115486[&model=LG+F{0.059/0.061/0.034/0.045/0.024/0.036/0.059/0.062/0.035/0.054/0.112/0.046/0.025/0.0476/0.046/0.070/0.064/0.017/0.031/0.06}]):0.1703326627,(((((((Bundibugyo_ebolavirus:0.0526067965,NC_014372TaiForestebolavirus:0.0478670483):0.0455889883,NC_002549Zaireebolavirus:0.0683024303):0.0366463699,NC_039345Bombaliebolavirus:0.1253945868):0.0428297699,NC_004161Restonebolavirus:0.1299718241):0.0316375085,NC_006432Sudanebolavirus:0.0900887787):0.2528694984,NC_016144_Lloviucuevavirus:0.3640635935):0.1981067560,(NC_055510Mengladianlovirus:0.2819453783,(NC_001608Marburgmarburgvirus:0.0180746773,NC_024781MarburgmarburgvirusRavn:0.0238981649):0.3046340712):0.3899536947):0.2872548657[&model=LG+F{0.058/0.053/0.041/0.043/0.019/0.041/0.048/0.048/0.027/0.063/0.124/0.052/0.018/0.051/0.049/0.083/0.069/0.015/0.046/0.052}]):3.4596014354);


Constraint treefile 2 with no presumptive LBA involving TAPV and XILV:

(NC_076735Oberlandvirus:0.8005304888,(NC_055176Wenlingthamnaconusseptentrionalis:0.2893705185,(NC_076734_LG+Fiwi_virus:0.1511077683,NC_076916_Kander_virus:0.1313453471):0.2551031398[&model=LG+F{0.056/0.058/0.033/0.053/0.029/0.030/0.058/0.066/0.036/0.046/0.116/0.045/0.027/0.043/0.048/0.083/0.059/0.012/0.030/0.073}]):0.4277396528,((NC_076535_Tapajosvirus:1.0021231719[&model=LG+F{0.065/0.059/0.042/0.034/0.027/0.042/0.051/0.052/0.027/0.067/0.122/0.041/0.022/0.046/0.044/0.079/0.066/0.017/0.047/0.054}],(((((((Bundibugyo_ebolavirus:0.0527236568,NC_014372TaiLG+Forestebolavirus:0.0479964174):0.0456770815,NC_002549Zaireebolavirus:0.0684838969):0.0367105512,NC_039345Bombaliebolavirus:0.1257055868):0.0429326700,NC_004161Restonebolavirus:0.1302590490):0.0315091034,NC_006432Sudanebolavirus:0.0904423411):0.2535167171,NC_016144_Lloviucuevavirus:0.3645430047):0.1992616386,(NC_055510Mengladianlovirus:0.2827014062,(NC_001608Marburgmarburgvirus:0.0180612519,NC_024781MarburgmarburgvirusRavn:0.0239644883):0.3047630792):0.3898819364):0.4210447968[&model=LG+F{0.058/0.053/0.041/0.043/0.019/0.041/0.048/0.048/0.027/0.063/0.124/0.052/0.018/0.051/0.049/0.083/0.069/0.015/0.046/0.052}]):0.1177307640,NC_055175Wenlingfrogfishfilovirus:1.0571857364[&model=LG+F{0.059/0.061/0.034/0.045/0.024/0.036/0.059/0.062/0.035/0.054/0.112/0.046/0.025/0.0476/0.046/0.070/0.064/0.017/0.031/0.06}]):3.4159938627);

Constraint treefile 3 with no presumptive LBA; long branches leading to TAPV and XILV reduced to 0.5 in length (about ½ the observed length)

(NC_076735Oberlandvirus:0.8005304888,(NC_055176Wenlingthamnaconusseptentrionalis:0.2893705185,(NC_076734_LG+Fiwi_virus:0.1511077683,NC_076916_Kander_virus:0.1313453471):0.2551031398[&model=LG+F{0.056/0.058/0.033/0.053/0.029/0.030/0.058/0.066/0.036/0.046/0.116/0.045/0.027/0.043/0.048/0.083/0.059/0.012/0.030/0.073}]):0.4277396528,((NC_076535_Tapajosvirus:0.5[&model=LG+F{0.065/0.059/0.042/0.034/0.027/0.042/0.051/0.052/0.027/0.067/0.122/0.041/0.022/0.046/0.044/0.079/0.066/0.017/0.047/0.054}],(((((((Bundibugyo_ebolavirus:0.0527236568,NC_014372TaiLG+Forestebolavirus:0.0479964174):0.0456770815,NC_002549Zaireebolavirus:0.0684838969):0.0367105512,NC_039345Bombaliebolavirus:0.1257055868):0.0429326700,NC_004161Restonebolavirus:0.1302590490):0.0315091034,NC_006432Sudanebolavirus:0.0904423411):0.2535167171,NC_016144_Lloviucuevavirus:0.3645430047):0.1992616386,(NC_055510Mengladianlovirus:0.2827014062,(NC_001608Marburgmarburgvirus:0.0180612519,NC_024781MarburgmarburgvirusRavn:0.0239644883):0.3047630792):0.3898819364):0.4210447968[&model=LG+F{0.058/0.053/0.041/0.043/0.019/0.041/0.048/0.048/0.027/0.063/0.124/0.052/0.018/0.051/0.049/0.083/0.069/0.015/0.046/0.052}]):0.1177307640,NC_055175Wenlingfrogfishfilovirus:0.5[&model=LG+F{0.059/0.061/0.034/0.045/0.024/0.036/0.059/0.062/0.035/0.054/0.112/0.046/0.025/0.0476/0.046/0.070/0.064/0.017/0.031/0.06}]):3.4159938627);


Command to estimate trees for simulated alignments:

iqtree-2.2.2.6-MacOSX/bin/iqtree2 -s /100_simulations_LBA_enforced_control_L_protein/sequences_20230807t193626/alignment.phy -S /100_simulations_LBA_enforced_control_L_protein/sequences_20230807t193626/alignment.nex -m LG+F+I+R4 -T AUTO -redo