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Vert_MGWE_Results
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Vert_MGWE_Results
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Information for the MGWE Analysis
################################################################
If any of this is wrong the analysis won't work, double check!!!!
You have set pxrmt to be in the path: pxrmt
You have set pxbp to be in the path: pxbp
You have set raxml to be in the path: raxmlHPC
The species in the relationship you are looking at are: alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis
You are testing this many Topos: 2
Your supermatrix is file called: ExampleConcat.fa
Your partition file is called: ExampleGenes.model
Your tree set file is (newick hopefully?): ExampleAllGeneTrees.tre
Running a test?: False
You're output folder is: Vert_MGWE_Info
Running it in verbose?: True
################################################################
You're Edge Info is in bp.log
You're Unique Trees are in Unique.tre
You're total genes: 248
##################Your Conflicts################
Conflict 0: alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis
Conflict 1: Gallus,Taeniopygia,alligator,caiman
Conflict 2: Ornithorhynchus,Homo,Monodelphis,podarcis,Anolis,python,phrynops,caretta,chelonoidis_nigra,emys_orbicularis
Conflict 3: Ornithorhynchus,Homo,Monodelphis,phrynops,caretta,chelonoidis_nigra,emys_orbicularis
Conflict 4: podarcis,Anolis,python,Gallus,Taeniopygia,alligator,caiman
###############Your Trees And their Conflicts##########
Tree: 0 Conflict: 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis
Tree: 1 Conflict: 1 Gallus,Taeniopygia,alligator,caiman
Tree: 2 Conflict: 1 Gallus,Taeniopygia,alligator,caiman
Tree: 2 Conflict: 2 Ornithorhynchus,Homo,Monodelphis,podarcis,Anolis,python,phrynops,caretta,chelonoidis_nigra,emys_orbicularis
Tree: 3 Conflict: 3 Ornithorhynchus,Homo,Monodelphis,phrynops,caretta,chelonoidis_nigra,emys_orbicularis
Tree: 4 Conflict: 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis
Tree: 5 Conflict: 1 Gallus,Taeniopygia,alligator,caiman
Tree: 5 Conflict: 4 podarcis,Anolis,python,Gallus,Taeniopygia,alligator,caiman
Tree: 6 Conflict: 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis
################################################################
#HERE ARE THE TAXA AND MISSING ONES FROM EACH GENE:
Gene_0: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,protopterus,python,
Gene_1: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,podarcis,python,
Gene_2: Has 11 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,podarcis,python,
Gene_3: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,phrynops,podarcis,protopterus,python,
Gene_4: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,
Gene_5: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,podarcis,python,
Gene_6: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,podarcis,protopterus,
Gene_7: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,podarcis,protopterus,python,
Gene_8: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,
Gene_9: Has 15 in it
These were removed from likelihood calc due to all missing data: alligator,
Gene_10: Has 11 in it
These were removed from likelihood calc due to all missing data: caiman,emys_orbicularis,podarcis,protopterus,python,
Gene_11: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,podarcis,protopterus,
Gene_12: Has 10 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_13: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,
Gene_14: Has 10 in it
These were removed from likelihood calc due to all missing data: caiman,chelonoidis_nigra,emys_orbicularis,podarcis,protopterus,python,
Gene_15: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,podarcis,python,
Gene_16: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,
Gene_17: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,
Gene_18: Has 13 in it
These were removed from likelihood calc due to all missing data: emys_orbicularis,protopterus,python,
Gene_19: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,podarcis,protopterus,
Gene_20: Has 12 in it
These were removed from likelihood calc due to all missing data: caiman,chelonoidis_nigra,podarcis,protopterus,
Gene_21: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,podarcis,protopterus,python,
Gene_22: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,emys_orbicularis,podarcis,python,
Gene_23: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,podarcis,
Gene_24: Has 9 in it
These were removed from likelihood calc due to all missing data: Ornithorhynchus,alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_25: Has 11 in it
These were removed from likelihood calc due to all missing data: chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,
Gene_26: Has 16 in it
These were removed from likelihood calc due to all missing data:
Gene_27: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,phrynops,podarcis,protopterus,python,
Gene_28: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_29: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,phrynops,podarcis,protopterus,python,
Gene_30: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,phrynops,
Gene_31: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,phrynops,
Gene_32: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,protopterus,
Gene_33: Has 15 in it
These were removed from likelihood calc due to all missing data: emys_orbicularis,
Gene_34: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,emys_orbicularis,phrynops,podarcis,python,
Gene_35: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,python,
Gene_36: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,protopterus,python,
Gene_37: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,
Gene_38: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_39: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,podarcis,protopterus,python,
Gene_40: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,phrynops,protopterus,
Gene_41: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,python,
Gene_42: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,python,
Gene_43: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,python,
Gene_44: Has 15 in it
These were removed from likelihood calc due to all missing data: caretta,
Gene_45: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,
Gene_46: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,podarcis,protopterus,python,
Gene_47: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_48: Has 12 in it
These were removed from likelihood calc due to all missing data: caiman,phrynops,protopterus,python,
Gene_49: Has 12 in it
These were removed from likelihood calc due to all missing data: caiman,chelonoidis_nigra,podarcis,protopterus,
Gene_50: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_51: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,podarcis,protopterus,python,
Gene_52: Has 14 in it
These were removed from likelihood calc due to all missing data: chelonoidis_nigra,phrynops,
Gene_53: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,python,
Gene_54: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,protopterus,python,
Gene_55: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,protopterus,python,
Gene_56: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,podarcis,
Gene_57: Has 13 in it
These were removed from likelihood calc due to all missing data: caiman,chelonoidis_nigra,emys_orbicularis,
Gene_58: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,
Gene_59: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_60: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,python,
Gene_61: Has 11 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,podarcis,protopterus,
Gene_62: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_63: Has 14 in it
These were removed from likelihood calc due to all missing data: chelonoidis_nigra,podarcis,
Gene_64: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,protopterus,
Gene_65: Has 8 in it
These were removed from likelihood calc due to all missing data: Ornithorhynchus,alligator,caretta,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_66: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,podarcis,protopterus,
Gene_67: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,phrynops,protopterus,python,
Gene_68: Has 16 in it
These were removed from likelihood calc due to all missing data:
Gene_69: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_70: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,
Gene_71: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,protopterus,python,
Gene_72: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,protopterus,python,
Gene_73: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_74: Has 11 in it
These were removed from likelihood calc due to all missing data: caiman,phrynops,podarcis,protopterus,python,
Gene_75: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,podarcis,protopterus,python,
Gene_76: Has 12 in it
These were removed from likelihood calc due to all missing data: caiman,emys_orbicularis,phrynops,podarcis,
Gene_77: Has 8 in it
These were removed from likelihood calc due to all missing data: Anolis,alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_78: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,
Gene_79: Has 13 in it
These were removed from likelihood calc due to all missing data: chelonoidis_nigra,podarcis,protopterus,
Gene_80: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,phrynops,podarcis,protopterus,python,
Gene_81: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,python,
Gene_82: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,podarcis,python,
Gene_83: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,python,
Gene_84: Has 15 in it
These were removed from likelihood calc due to all missing data: alligator,
Gene_85: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_86: Has 13 in it
These were removed from likelihood calc due to all missing data: emys_orbicularis,podarcis,python,
Gene_87: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,
Gene_88: Has 11 in it
These were removed from likelihood calc due to all missing data: caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_89: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,phrynops,podarcis,python,
Gene_90: Has 12 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,podarcis,protopterus,
Gene_91: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,podarcis,python,
Gene_92: Has 9 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_93: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,protopterus,python,
Gene_94: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_95: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,protopterus,python,
Gene_96: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,phrynops,podarcis,protopterus,python,
Gene_97: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,podarcis,protopterus,python,
Gene_98: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,phrynops,podarcis,python,
Gene_99: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,podarcis,protopterus,python,
Gene_100: Has 10 in it
These were removed from likelihood calc due to all missing data: caiman,chelonoidis_nigra,emys_orbicularis,podarcis,protopterus,python,
Gene_101: Has 11 in it
These were removed from likelihood calc due to all missing data: caiman,chelonoidis_nigra,podarcis,protopterus,python,
Gene_102: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,emys_orbicularis,phrynops,protopterus,
Gene_103: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,python,
Gene_104: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,
Gene_105: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,protopterus,
Gene_106: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,podarcis,python,
Gene_107: Has 11 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,podarcis,protopterus,python,
Gene_108: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,protopterus,
Gene_109: Has 16 in it
These were removed from likelihood calc due to all missing data:
Gene_110: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,
Gene_111: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,podarcis,python,
Gene_112: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,protopterus,
Gene_113: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,protopterus,python,
Gene_114: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,phrynops,podarcis,python,
Gene_115: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,protopterus,
Gene_116: Has 10 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_117: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,python,
Gene_118: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,phrynops,podarcis,protopterus,
Gene_119: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,podarcis,protopterus,python,
Gene_120: Has 11 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,phrynops,podarcis,
Gene_121: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,podarcis,protopterus,
Gene_122: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_123: Has 15 in it
These were removed from likelihood calc due to all missing data: alligator,
Gene_124: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,protopterus,python,
Gene_125: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,podarcis,protopterus,
Gene_126: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,podarcis,protopterus,
Gene_127: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_128: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,protopterus,
Gene_129: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_130: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,podarcis,python,
Gene_131: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,
Gene_132: Has 13 in it
These were removed from likelihood calc due to all missing data: caretta,chelonoidis_nigra,podarcis,
Gene_133: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,python,
Gene_134: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,python,
Gene_135: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,protopterus,
Gene_136: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,protopterus,
Gene_137: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,python,
Gene_138: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,python,
Gene_139: Has 11 in it
These were removed from likelihood calc due to all missing data: chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,python,
Gene_140: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_141: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,podarcis,protopterus,
Gene_142: Has 13 in it
These were removed from likelihood calc due to all missing data: chelonoidis_nigra,emys_orbicularis,podarcis,
Gene_143: Has 15 in it
These were removed from likelihood calc due to all missing data: alligator,
Gene_144: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_145: Has 15 in it
These were removed from likelihood calc due to all missing data: alligator,
Gene_146: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,phrynops,podarcis,protopterus,python,
Gene_147: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_148: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_149: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,
Gene_150: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_151: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,
Gene_152: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,protopterus,
Gene_153: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,phrynops,podarcis,protopterus,python,
Gene_154: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,phrynops,
Gene_155: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,podarcis,protopterus,python,
Gene_156: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,phrynops,
Gene_157: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,protopterus,python,
Gene_158: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,protopterus,
Gene_159: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_160: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_161: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_162: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_163: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,protopterus,
Gene_164: Has 16 in it
These were removed from likelihood calc due to all missing data:
Gene_165: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,protopterus,python,
Gene_166: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,podarcis,protopterus,python,
Gene_167: Has 10 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,emys_orbicularis,phrynops,podarcis,python,
Gene_168: Has 13 in it
These were removed from likelihood calc due to all missing data: caiman,podarcis,protopterus,
Gene_169: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_170: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,protopterus,python,
Gene_171: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,python,
Gene_172: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,python,
Gene_173: Has 13 in it
These were removed from likelihood calc due to all missing data: emys_orbicularis,podarcis,protopterus,
Gene_174: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,
Gene_175: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_176: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_177: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,podarcis,python,
Gene_178: Has 10 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,phrynops,podarcis,protopterus,python,
Gene_179: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,
Gene_180: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,podarcis,protopterus,
Gene_181: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,emys_orbicularis,phrynops,protopterus,python,
Gene_182: Has 14 in it
These were removed from likelihood calc due to all missing data: emys_orbicularis,phrynops,
Gene_183: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,protopterus,python,
Gene_184: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,
Gene_185: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,protopterus,python,
Gene_186: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,emys_orbicularis,podarcis,protopterus,python,
Gene_187: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,podarcis,python,
Gene_188: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,protopterus,python,
Gene_189: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,podarcis,
Gene_190: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,podarcis,protopterus,python,
Gene_191: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_192: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_193: Has 10 in it
These were removed from likelihood calc due to all missing data: caiman,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,
Gene_194: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,podarcis,python,
Gene_195: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,protopterus,
Gene_196: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,python,
Gene_197: Has 9 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_198: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,python,
Gene_199: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_200: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,protopterus,python,
Gene_201: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_202: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,protopterus,
Gene_203: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,podarcis,protopterus,python,
Gene_204: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,podarcis,protopterus,python,
Gene_205: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,podarcis,protopterus,python,
Gene_206: Has 15 in it
These were removed from likelihood calc due to all missing data: alligator,
Gene_207: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,python,
Gene_208: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,protopterus,python,
Gene_209: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,
Gene_210: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_211: Has 14 in it
These were removed from likelihood calc due to all missing data: caretta,protopterus,
Gene_212: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,protopterus,
Gene_213: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,podarcis,protopterus,python,
Gene_214: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,
Gene_215: Has 14 in it
These were removed from likelihood calc due to all missing data: emys_orbicularis,python,
Gene_216: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_217: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_218: Has 9 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_219: Has 12 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,protopterus,python,
Gene_220: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_221: Has 10 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_222: Has 12 in it
These were removed from likelihood calc due to all missing data: caiman,podarcis,protopterus,python,
Gene_223: Has 11 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,phrynops,podarcis,python,
Gene_224: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_225: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,phrynops,podarcis,protopterus,python,
Gene_226: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,protopterus,python,
Gene_227: Has 16 in it
These were removed from likelihood calc due to all missing data:
Gene_228: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,protopterus,
Gene_229: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,
Gene_230: Has 15 in it
These were removed from likelihood calc due to all missing data: chelonoidis_nigra,
Gene_231: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_232: Has 14 in it
These were removed from likelihood calc due to all missing data: alligator,protopterus,
Gene_233: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,phrynops,
Gene_234: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_235: Has 13 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,python,
Gene_236: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_237: Has 11 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,podarcis,protopterus,
Gene_238: Has 10 in it
These were removed from likelihood calc due to all missing data: caiman,caretta,chelonoidis_nigra,phrynops,podarcis,python,
Gene_239: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,emys_orbicularis,podarcis,protopterus,python,
Gene_240: Has 10 in it
These were removed from likelihood calc due to all missing data: caiman,chelonoidis_nigra,phrynops,podarcis,protopterus,python,
Gene_241: Has 15 in it
These were removed from likelihood calc due to all missing data: podarcis,
Gene_242: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,emys_orbicularis,podarcis,protopterus,python,
Gene_243: Has 12 in it
These were removed from likelihood calc due to all missing data: caiman,podarcis,protopterus,python,
Gene_244: Has 14 in it
These were removed from likelihood calc due to all missing data: caiman,podarcis,
Gene_245: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,chelonoidis_nigra,emys_orbicularis,phrynops,podarcis,protopterus,python,
Gene_246: Has 11 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,chelonoidis_nigra,podarcis,python,
Gene_247: Has 9 in it
These were removed from likelihood calc due to all missing data: alligator,caretta,emys_orbicularis,phrynops,podarcis,protopterus,python,
#######################Gene Counts###############################
Conflict 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 91
Conflict 1 Gallus,Taeniopygia,alligator,caiman: 144
Conflict 2 Ornithorhynchus,Homo,Monodelphis,podarcis,Anolis,python,phrynops,caretta,chelonoidis_nigra,emys_orbicularis:
Conflict 3 Ornithorhynchus,Homo,Monodelphis,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 13
Conflict 4 podarcis,Anolis,python,Gallus,Taeniopygia,alligator,caiman:
#######################Site Counts###############################
Conflict 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 66315
Conflict 1 Gallus,Taeniopygia,alligator,caiman: 110727
Conflict 2 Ornithorhynchus,Homo,Monodelphis,podarcis,Anolis,python,phrynops,caretta,chelonoidis_nigra,emys_orbicularis:
Conflict 3 Ornithorhynchus,Homo,Monodelphis,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 9984
Conflict 4 podarcis,Anolis,python,Gallus,Taeniopygia,alligator,caiman:
#######################Paramater Info############################
Parameters of your regular old supermatrix: 2261
Parameters used for the Edge analysis: 7186
#######################Your Likelihoods##########################
Tree 0: -1047406.056279
Tree 1: -1047410.075015
Indv BrLen 0: -1031489.817195
Indv BrLen 1: -1031453.355229
Edge 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: -1031423.67415
Edge 1 Gallus,Taeniopygia,alligator,caiman: -1031294.019851
Edge 2 Ornithorhynchus,Homo,Monodelphis,podarcis,Anolis,python,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: -1041062.404812
Edge 3 Ornithorhynchus,Homo,Monodelphis,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: -1033745.134682
Edge 4 podarcis,Anolis,python,Gallus,Taeniopygia,alligator,caiman: -1032083.686971
The Best Likelihood is: -1031294.019851
#####################Your AIC Scores##########################
Tree 0: 2099334.112558
Tree 1: 2099342.15003
Indv BrLen 0: 2077351.63439
Indv BrLen 1: 2077278.710458
Edge 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 2077219.3483
Edge 1 Gallus,Taeniopygia,alligator,caiman: 2076960.039702
Edge 2 Ornithorhynchus,Homo,Monodelphis,podarcis,Anolis,python,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 2096496.809624
Edge 3 Ornithorhynchus,Homo,Monodelphis,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 2081862.269364
Edge 4 podarcis,Anolis,python,Gallus,Taeniopygia,alligator,caiman: 2078539.373942
The Best AIC is: 2076960.039702
#######################Your AICc Scores########################
Tree 0: 2099389.4737972
Tree 1: 2099397.5112692
Indv BrLen 0: 2077925.99014153
Indv BrLen 1: 2077853.06620954
Edge 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 2077793.70405153
Edge 1 Gallus,Taeniopygia,alligator,caiman: 2077534.39545353
Edge 2 Ornithorhynchus,Homo,Monodelphis,podarcis,Anolis,python,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 2097071.16537553
Edge 3 Ornithorhynchus,Homo,Monodelphis,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 2082436.62511553
Edge 4 podarcis,Anolis,python,Gallus,Taeniopygia,alligator,caiman: 2079113.72969353
The Best AICc is: 2077534.39545353
###################Your Delta AIC Scores#######################
Tree 0: 22374.0728559988
Tree 1: 22382.1103279991
Indv BrLen 0: 391.594687999692
Indv BrLen 1: 318.670756000793
Edge 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 259.308598000556
Edge 1 Gallus,Taeniopygia,alligator,caiman: 0
Edge 2 Ornithorhynchus,Homo,Monodelphis,podarcis,Anolis,python,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 19536.7699219994
Edge 3 Ornithorhynchus,Homo,Monodelphis,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 4902.22966199834
Edge 4 podarcis,Anolis,python,Gallus,Taeniopygia,alligator,caiman: 1579.33424000023
##################Your Delta AICc Scores########################
Tree 0: 21855.0783436678
Tree 1: 21863.1158156681
Indv BrLen 0: 391.594687999692
Indv BrLen 1: 318.670756000793
Edge 0 alligator,caiman,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 259.308598000556
Edge 1 Gallus,Taeniopygia,alligator,caiman: 0
Edge 2 Ornithorhynchus,Homo,Monodelphis,podarcis,Anolis,python,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 19536.7699219994
Edge 3 Ornithorhynchus,Homo,Monodelphis,phrynops,caretta,chelonoidis_nigra,emys_orbicularis: 4902.22966199834
Edge 4 podarcis,Anolis,python,Gallus,Taeniopygia,alligator,caiman: 1579.33424000023