Hi:

I plot taxonomic developmental tree. When I read the data using read.tree, species name with bracket appears error, they are ignoring bracket.
mytree<-read.tree("((((Clostridioides_difficile:1)Clostridium:1)Clostridiaceae_1:1,(Agathobacter:1,(Anaerostipes_hadrus:1)Anaerostipes:1,(Ruminococcus_sp._5_1_39BFAA:1,uncultured_Ruminococcus_sp.:1)Blautia:1,(Coprococcus_comes:1)Coprococcus:1,(Dorea_formicigenerans:1)Dorea:1,(uncultured_organism:1)Fusicatenibacter:1,(Bacteroides_galacturonicus:1)Lachnospira:1,Lachnospiraceae_ND3007_group:1,Lachnospiraceae_UCG-001:1,(uncultured_organism:1)Lachnospiraceae_UCG-004:1,Roseburia:1,[Eubacterium]_eligens_group:1,[Eubacterium]_hallii_group:1,[Eubacterium]_ventriosum_group:1,(Ruminococcus_gnavus:1)[Ruminococcus]_gnavus_group:1,(Ruminococcus_lactaris:1)[Ruminococcus]_torques_group:1)Lachnospiraceae:1,(Romboutsia:1)Peptostreptococcaceae:1,((uncultured_organism:1)Butyricicoccus:1,(Faecalibacterium_prausnitzii:1)Faecalibacterium:1,Ruminococcaceae_UCG-002:1,Ruminococcaceae_UCG-003:1,(uncultured_bacterium:1)Ruminococcaceae_UCG-004:1,(uncultured_organism:1)Ruminococcaceae_UCG-005:1,(uncultured_organism:1)Ruminococcaceae_UCG-013:1,(Ruminococcus_bromii:1)Ruminococcus:1,Subdoligranulum:1,(uncultured_organism:1)UBA1819:1,[Eubacterium]_coprostanoligenes_group:1)Ruminococcaceae:1,(Phascolarctobacterium:1)Veillonellaceae:1)Clostridiales:1);")
mytree_data<-fortify(mytree)
mytree_data$label

restult: nums 14/15/16/30/44/45 species name all false.

[1] "Clostridioides_difficile"     "Agathobacter"                

 [3] "Anaerostipes_hadrus"          "Ruminococcus_sp._5_1_39BFAA" 

 [5] "uncultured_Ruminococcus_sp."  "Coprococcus_comes"           

 [7] "Dorea_formicigenerans"        "uncultured_organism"         

 [9] "Bacteroides_galacturonicus"   "Lachnospiraceae_ND3007_group"

[11] "Lachnospiraceae_UCG-001"      "uncultured_organism"         

[13] "Roseburia"                    "_eligens_group"              

[15] "_hallii_group"                "_ventriosum_group"           

[17] "Ruminococcus_gnavus"          "Ruminococcus_lactaris"       

[19] "Romboutsia"                   "uncultured_organism"         

[21] "Faecalibacterium_prausnitzii" "Ruminococcaceae_UCG-002"     

[23] "Ruminococcaceae_UCG-003"      "uncultured_bacterium"        

[25] "uncultured_organism"          "uncultured_organism"         

[27] "Ruminococcus_bromii"          "Subdoligranulum"             

[29] "uncultured_organism"          "_coprostanoligenes_group"    

[31] "Phascolarctobacterium"        ""                            

[33] "Clostridiales"                "Clostridiaceae_1"            

[35] "Clostridium"                  "Lachnospiraceae"             

[37] "Anaerostipes"                 "Blautia"                     

[39] "Coprococcus"                  "Dorea"                       

[41] "Fusicatenibacter"             "Lachnospira"                 

[43] "Lachnospiraceae_UCG-004"      "_gnavus_group"               

[45] "_torques_group"               "Peptostreptococcaceae"       

[47] "Ruminococcaceae"              "Butyricicoccus"              

[49] "Faecalibacterium"             "Ruminococcaceae_UCG-004"     

[51] "Ruminococcaceae_UCG-005"      "Ruminococcaceae_UCG-013"     

[53] "Ruminococcus"                 "UBA1819"                     

[55] "Veillonellaceae"