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Hi,
I'm doing an undergraduate research project and I'm trying to figure out what these values mean alongside a phylogenetic tree that's been constructed using ClustalOmega (https://www.ebi.ac.uk/Tools/msa/clustalo/). Here are the results I get when I put in a few proteins from the PDB (attached as a pdf).
Really would appreciate any help!
Here's another set of information I get when I plug in the data with the values included as well (don't know if that helps at all
( ( ( ( ( ( ( Porcine_Transmissible_Gastroenteritis_Coronavirus_strain_Purdue|3mp2:0.36426, ( SARS-related_Coronavirus|2fe8:0.34567, Human_Betacoronavirus_2c_EMC/2012__MERS_|4rna:0.34640) :0.03202) :0.05354, Turnip_Mosaic_Virus|3rnv:0.42225) :0.02581, ( ( Chikungya_Virus|3trk:0.40225, Staphylococcus_Virus_K|4ct3:0.39775) :0.02208, ( Yellow_Fever_Virus|1yks:0.24815, ( Dengue_Virus|2jlq:0.16628, ( Kunjin_Virus__West_Nile_Virus_|2qeq:0.08943, Murray_Valley_Encephalitis_Virus|2v8o:0.08799) :0.07748) :0.07761) :0.16839) :0.02547) :0.00817, ( Hepatitis_C_Virus|2hd0:0.39557, ( Human_Rhinovirus_A2|5fx6:0.26869, ( Enterovirus_D68|3zve:0.17701, ( Enterovirus_C|2ijd:0.02995, Human_Poliovirus_1_Mahoney|4dcd:-0.00810) :0.16830) :0.09329) :0.05023) :0.07198) :0.01009, ( ( ( Blotched_Snakehead_Virus|2gef:0.39036, ( Human_Coronavirus_NL63|2vri:0.34202, Middle_East_Respiratory_Syndrome-related_Coronavirus|5hih:0.33463) :0.06929) :0.04091, ( Infectious_Bronchitis_Virus__Avian_Coronavirus_|2q6d:0.29697, ( Tylonycteris_Bat_Coronavirus_HKU4|2yna:0.26516, ( Porcine_Transmissible_Gastroenteritis_Coronavirus_strain_Purdue|4f49:0.20852, ( Human_Coronavirus_NL63|3tlo:0.16280, Porcine_Epidemic_Diarrhea_Virus|4xfq:0.15508) :0.03584) :0.04892) :0.03033) :0.12381) :0.00437, ( ( ( Murray_Valley_Encephalitis_Virus|2px2:0.39281, Classical_Swine_Fever_Virus|4cbh:0.37249) :0.01609, ( Mason-Pfizer_Monkey_Virus|3sqf:0.40046, ( ( ( Rous_Sarcoma_Virus|2rsp:0.26965, Sesbania_Mosaic_Virus|1zyo:0.23035) :0.09476, ( Simian_Immunodeficiency_Virus|1az5:0.31836, Equine_Infectious_Anemia_Virus|1fmb:0.31429) :0.03206) :0.04596, Feline_Immunodeficiency_Virus|4fiv:0.39917) :0.00272) :0.03608) :0.00785, Infectious_Pancreatic_Necrosis_Virus|2pnl:0.42983) :0.01305) :0.02076) :0.00861, ( Human_Pathogenic_Astrovirus__Mamastrovirus_1_|2w5e:0.39085, ( Equine_Arteritis_Virus|1mbm:0.30756, Porcine_Reproductive_and_Respiratory_Syndrome_Virus|3fan:0.33346) :0.06693) :0.02580) :0.00341, ( ( ( ( Pestivirus_Strain_D32/00_HoBi|3zfp:0.11977, ( Classical_Swine_Fever_Virus_-_Alfort/187|4h9j:0.09687, Tellina_Virus_1|3p06:-0.09687) :0.03901) :0.24196, ( Human_Enterovirus_71|3w95:0.01789, Coxsackievirus_A16__strain_Tainan/5079/98_|4mg3:0.03039) :0.31918) :0.04136, ( Foot-and-mouth_Disease_Virus|2bhg:0.09450, Foot-and-Mouth_Disease_Virus_-_type_SAT_2|5hm2:0.10646) :0.26567) :0.03129, ( ( ( Herpes_Simplex_Virus_Type_II__Human_Alphaherpesvirus_2_|1at3:0.23583, ( Varicella-Zoster_Virus__Human_alphaherpesvirus_3_|1vzv:0.21513, Suid_Alphaherpesvirus_1|4v08:0.20039) :0.01444) :0.06820, ( Epstein-Barr_Virus__Human_gammaherpesvirus_4_|1o6e:0.24908, ( Human_Cytomegalovirus_Protease__Human_betaherpesvirus_5_|1wpo:0.17539, SARS_Coronavirus|3ebn:-0.17539) :0.08354) :0.08567) :0.08207, Enterobacteria_Phage_T4|5jbl:0.39007) :0.02434) :0.01192, ( ( ( Porcine_Reproductive_and_Respiratory_Syndrome_Virus|3ifu:0.00949, Norovirus_Hu/1968/US|5dgj:-0.00949) :0.11662, Murine_Norovirus_1|4ash:0.10196) :0.31023, Cavally_Virus|5lac:0.43446) :0.00767);
I'm doing an undergraduate research project and I'm trying to figure out what these values mean alongside a phylogenetic tree that's been constructed using ClustalOmega (https://www.ebi.ac.uk/Tools/msa/clustalo/). Here are the results I get when I put in a few proteins from the PDB (attached as a pdf).
Really would appreciate any help!
Here's another set of information I get when I plug in the data with the values included as well (don't know if that helps at all
( ( ( ( ( ( ( Porcine_Transmissible_Gastroenteritis_Coronavirus_strain_Purdue|3mp2:0.36426, ( SARS-related_Coronavirus|2fe8:0.34567, Human_Betacoronavirus_2c_EMC/2012__MERS_|4rna:0.34640) :0.03202) :0.05354, Turnip_Mosaic_Virus|3rnv:0.42225) :0.02581, ( ( Chikungya_Virus|3trk:0.40225, Staphylococcus_Virus_K|4ct3:0.39775) :0.02208, ( Yellow_Fever_Virus|1yks:0.24815, ( Dengue_Virus|2jlq:0.16628, ( Kunjin_Virus__West_Nile_Virus_|2qeq:0.08943, Murray_Valley_Encephalitis_Virus|2v8o:0.08799) :0.07748) :0.07761) :0.16839) :0.02547) :0.00817, ( Hepatitis_C_Virus|2hd0:0.39557, ( Human_Rhinovirus_A2|5fx6:0.26869, ( Enterovirus_D68|3zve:0.17701, ( Enterovirus_C|2ijd:0.02995, Human_Poliovirus_1_Mahoney|4dcd:-0.00810) :0.16830) :0.09329) :0.05023) :0.07198) :0.01009, ( ( ( Blotched_Snakehead_Virus|2gef:0.39036, ( Human_Coronavirus_NL63|2vri:0.34202, Middle_East_Respiratory_Syndrome-related_Coronavirus|5hih:0.33463) :0.06929) :0.04091, ( Infectious_Bronchitis_Virus__Avian_Coronavirus_|2q6d:0.29697, ( Tylonycteris_Bat_Coronavirus_HKU4|2yna:0.26516, ( Porcine_Transmissible_Gastroenteritis_Coronavirus_strain_Purdue|4f49:0.20852, ( Human_Coronavirus_NL63|3tlo:0.16280, Porcine_Epidemic_Diarrhea_Virus|4xfq:0.15508) :0.03584) :0.04892) :0.03033) :0.12381) :0.00437, ( ( ( Murray_Valley_Encephalitis_Virus|2px2:0.39281, Classical_Swine_Fever_Virus|4cbh:0.37249) :0.01609, ( Mason-Pfizer_Monkey_Virus|3sqf:0.40046, ( ( ( Rous_Sarcoma_Virus|2rsp:0.26965, Sesbania_Mosaic_Virus|1zyo:0.23035) :0.09476, ( Simian_Immunodeficiency_Virus|1az5:0.31836, Equine_Infectious_Anemia_Virus|1fmb:0.31429) :0.03206) :0.04596, Feline_Immunodeficiency_Virus|4fiv:0.39917) :0.00272) :0.03608) :0.00785, Infectious_Pancreatic_Necrosis_Virus|2pnl:0.42983) :0.01305) :0.02076) :0.00861, ( Human_Pathogenic_Astrovirus__Mamastrovirus_1_|2w5e:0.39085, ( Equine_Arteritis_Virus|1mbm:0.30756, Porcine_Reproductive_and_Respiratory_Syndrome_Virus|3fan:0.33346) :0.06693) :0.02580) :0.00341, ( ( ( ( Pestivirus_Strain_D32/00_HoBi|3zfp:0.11977, ( Classical_Swine_Fever_Virus_-_Alfort/187|4h9j:0.09687, Tellina_Virus_1|3p06:-0.09687) :0.03901) :0.24196, ( Human_Enterovirus_71|3w95:0.01789, Coxsackievirus_A16__strain_Tainan/5079/98_|4mg3:0.03039) :0.31918) :0.04136, ( Foot-and-mouth_Disease_Virus|2bhg:0.09450, Foot-and-Mouth_Disease_Virus_-_type_SAT_2|5hm2:0.10646) :0.26567) :0.03129, ( ( ( Herpes_Simplex_Virus_Type_II__Human_Alphaherpesvirus_2_|1at3:0.23583, ( Varicella-Zoster_Virus__Human_alphaherpesvirus_3_|1vzv:0.21513, Suid_Alphaherpesvirus_1|4v08:0.20039) :0.01444) :0.06820, ( Epstein-Barr_Virus__Human_gammaherpesvirus_4_|1o6e:0.24908, ( Human_Cytomegalovirus_Protease__Human_betaherpesvirus_5_|1wpo:0.17539, SARS_Coronavirus|3ebn:-0.17539) :0.08354) :0.08567) :0.08207, Enterobacteria_Phage_T4|5jbl:0.39007) :0.02434) :0.01192, ( ( ( Porcine_Reproductive_and_Respiratory_Syndrome_Virus|3ifu:0.00949, Norovirus_Hu/1968/US|5dgj:-0.00949) :0.11662, Murine_Norovirus_1|4ash:0.10196) :0.31023, Cavally_Virus|5lac:0.43446) :0.00767);