server.R

#
# This is the server logic of a Shiny web application. You can run the 
# application by clicking 'Run App' above.
#
# Find out more about building applications with Shiny here:
# 
#    http://shiny.rstudio.com/
#


## Load necessary packages
if (!require("phytools")) {
   install.packages("phytools", dependencies = TRUE)
   library(phytools)
   }

# Define server logic
shinyServer(function(input, output, session) {
  #############
  ### FUNGI ###
  #############
  ## read in file reactively
  FUNGIdata <- eventReactive(input$FUNGIgo, { 
    req(input$FUNGIfile)
    inFile <- input$FUNGIfile
    FUNGItaxa.list<-read.table(inFile$datapath)
    return(FUNGItaxa.list)
    })

  ## read in tree based on selected tree
  FUNGItree <- eventReactive(input$FUNGIgo, {
    if (input$FUNGIphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
      FUNGItree <- read.tree("./Data/Aspergillaceae_fig1_Steenwyk_etal_2018.tre")
    } else if (input$FUNGIphyloSelect == "Saccharomycotina, 86 taxa - Shen et al. 2016") {
      FUNGItree <- read.tree("./Data/Saccharomycotina_fig3_Shen_etal_2016.tre")
    } else if (input$FUNGIphyloSelect == "Saccharomycotina, 332 taxa - Shen et al. 2018") {
      FUNGItree <- read.tree("./Data/Saccharomycotina_fig2_Shen_etal_2018.tre")
    } else if (input$FUNGIphyloSelect == "Saccharomyces cerevisiae, 1,011 strains - Peter et al. 2018") {
      FUNGItree <- read.tree("./Data/Saccharomyces_cerevisiae_fig1_Peter_etal_2018.tre") 
    } else if (input$FUNGIphyloSelect == "Cryptococcus neoformans, 387 strains - Desjardins et al. 2017") {
      FUNGItree <- read.tree("./Data/Cryptococcus_neoformans_fig1_Desjardins_etal_2017.tre")  
    } else if (input$FUNGIphyloSelect == "Fungi, 214 taxa - James et al. 2006") {
      FUNGItree <- read.nexus("./Data/Fungi_fig1_James_etal_2006.nex.tre")  
    } else if (input$FUNGIphyloSelect == "Agaricomycetes, 5,284 taxa - Varga et al. 2019") {
      FUNGItree <- read.nexus("./Data/Fungi_fig1_Varga_etal_2019.nex.tre")  
    } else if (input$FUNGIphyloSelect == "Fungi, 60 taxa - Nagy et al. 2014") {
      FUNGItree <- read.tree("./Data/Fungi_fig1_Nagy_etal_2014.tre")  
    } else if (input$FUNGIphyloSelect == "Tree of life, 3,083 taxa - Hug et al. 2016") {
      FUNGItree <- read.tree("./Data/Tree_of_Life_fig1_Hug_etal_2016.tre")
    } else if (input$FUNGIphyloSelect == "Ascomycota, 1,113 taxa - Shen et al. 2020") {
      FUNGItree <- read.tree("./Data/Ascomycota_fig1_Shen_etal_2020.tre")  
    } else 
      FUNGItree <- read.tree("./Data/Aspergillaceae_fig1_Steenwyk_etal_2018.tre")
  })

  ## select outgroup labels based on selected tree
  FUNGIoutgroup.labels <- eventReactive(input$FUNGIgo, {input$FUNGIphyloSelect
    if (input$FUNGIphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
      FUNGIoutgroup.labels<-c("Neurospora_crassa","Microsporum_canis","Uncinocarpus_reesii","Trichophyton_rubrum","Basipetospora_chlamydospora","Coccidioides_posadasii","Paracoccidioides_brasiliensis","Trichoderma_reesei","Coccidioides_immitis","Histoplasma_capsulatum","Talaromyces_occitanis","Talaromyces_marneffei")
      }
      else if (input$FUNGIphyloSelect == "Saccharomycotina, 86 taxa - Shen et al. 2016") {
      FUNGIoutgroup.labels<-c("Schizosaccharomyces_pombe","Arthrobotrys_oligospora","Neurospora_crassa","Fusarium_graminearum","Geotrichum_candidum_3C", "Botrytis_cinerea", "Sclerotinia_sclerotiorum", "Stagonospora_nodorum", "Aspergillus_nidulans","Xylona_heveae")
      }
      else if (input$FUNGIphyloSelect == "Saccharomycotina, 332 taxa - Shen et al. 2018") {
      FUNGIoutgroup.labels<-c("Saitoella_complicata","Schizosaccharomyces_pombe","Arthrobotrys_oligospora","Fusarium_graminearum","Neurospora_crassa", "Sclerotinia_sclerotiorum", "Botrytis_cinerea", "Stagonospora_nodorum", "Aspergillus_nidulans","Xylona_heveae", "Coccidioides_immitis")
      }
      else if (input$FUNGIphyloSelect == "Saccharomyces cerevisiae, 1,011 strains - Peter et al. 2018") {
      FUNGIoutgroup.labels<-c("AMH","CEG","CEI")
      }
      else if (input$FUNGIphyloSelect == "Cryptococcus neoformans, 387 strains - Desjardins et al. 2017") {
      FUNGIoutgroup.labels<-c("8-1","AD3-11a","AD3-9a","AD5-67a","C12","C2","C45","LP-RSA1684","MW-RSA1327","MW-RSA3956","MW-RSA4119","MW_RSA852","PMHc1023.ENR","T4","Ug2462","WM626")
      }
      else if (input$FUNGIphyloSelect == "Fungi, 214 taxa - James et al. 2006") {
      FUNGIoutgroup.labels<-c("Chlamydomonas_reinhardtii","Oryza_sativa","Arabidopsis_thaliana","Populus_trichocarpa")
      }
      else if (input$FUNGIphyloSelect == "Agaricomycetes, 5,284 taxa - Varga et al. 2019") {
      FUNGIoutgroup.labels<-c("Tremella_polyporina", "Syzygospora_effibulata", "Cryptococcus_podzolicus", "Asterotremella_humicola", "Trichosporon_scarabaeorum", "Trichosporon_domesticum", "Trichosporon_brassicae", "Trichosporon_montevideense", "Trichosporon_mycotoxinivorans", "Trichosporon_loubieri", "Trichosporon_multisporum", "Trichosporon_veenhuisii", "Trichosporon_laibachii", "Trichosporon_gracile", "Trichosporon_dulcitum", "Trichosporon_vadense", "Cryptococcus_humicola", "Trichosporon_wieringae", "Trichosporon_gamsii", "Trichosporon_sporotrichoides", "Trichosporon_porosum", "Trichosporon_inkin", "Trichosporon_coremiiforme", "Trichosporon_faecale", "Trichosporon_japonicum", "Trichosporon_jirovecii", "Trichosporon_debeurmannianum", "Trichosporon_dermatis", "Trichosporon_moniliiforme", "Tremella_globispora", "Cryptococcus_bacillisporus", "Cryptococcus_gattii", "Cryptococcus_neoformans", "Cryptococcus_neoformansvargrubii", "Tsuchiyaea_wingfieldii", "Cryptococcus_amylolentus", "Filobasidiella_depauperata", "Cryptococcus_dejecticola", "Cryptococcus_bestiolae", "Bullera_dendrophila", "Cryptococcus_heveanensis", "Derxomyces_linzhiensis", "Derxomyces_anomala", "Derxomyces_simaoensis", "Derxomyces_komagatae", "Derxomyces_schimicola", "Derxomyces_pseudoschimicola", "Dioszegia_takashimae", "Derxomyces_pseudocylindrica", "Derxomyces_wuzhishanensis", "Derxomyces_hainanensis", "Derxomyces_mrakii", "Derxomyces_boninensis", "Derxomyces_qinlingensis", "Derxomyces_pseudohuiaensis", "Derxomyces_cylindrica", "Derxomyces_waltii", "Derxomyces_nakasei", "Derxomyces_boekhoutii", "Derxomyces_huiaensis", "Derxomyces_hubeiensis", "Derxomyces_yunnanensis", "Sirobasidium_magnum", "Tremella_parmeliarum", "Trimorphomyces_nebularis", "Tremella_fuciformis", "Tremella_brasiliensis", "Tremella_indecorata", "Cryptococcus_laurentii", "Cryptococcus_rajasthanensis", "Cryptococcus_cellulolyticus", "Sirobasidium_brefeldianum", "Tremella_caloplacae", "Tremella_dendrographae", "Tremella_candelariellae", "Tremella_giraffa", "Tremella_cetrariicola", "Biatoropsis_usnearum", "Tremella_tuckerae", "Tremella_coppinsii", "Tremella_wirthii", "Tremella_pertusariae", "Tremella_ramalinae", "Tremella_lichenicola", "Tremella_everniae", "Tremella_hypogymniae", "Tremella_encephala", "Tremella_phaeophysciae", "Tremella_leptogii", "Tremella_lobariacearum", "Tremella_nephromatis", "Tremella_cladoniae", "Tremella_haematommatis", "Tremella_foliacea", "Tremella_mesenterica", "Fibulobasidium_inconspicuum", "Cryptococcus_magnus", "Syzygospora_pallida", "Syzygospora_alba", "Syzygospora_physciacearum", "Syzygospora_bachmannii", "Cryptococcus_terreus", "Cryptococcus_terricola", "Cryptococcus_aerius", "Cryptococcus_saitoi")
      }
      else if (input$FUNGIphyloSelect == "Fungi, 60 taxa - Nagy et al. 2014") {
      FUNGIoutgroup.labels<-c("Dicdi", "Enthi", "Thetr", "Monbr", "Salro", "Traho", "Enccu", "Antlo")
      }
      else if (input$FUNGIphyloSelect == "Ascomycota, 1,113 taxa - Shen et al. 2020") {
      FUNGIoutgroup.labels<-c("Malassezia_globosa", "Cryptococcus_neoformans", "Mixia_osmundae", "Phanerochaete_chrysosporium", "Microbotryum_violaceum", "Ustilago_maydis")
      }
      else {
      FUNGIoutgroup.labels<-c("Neurospora_crassa","Microsporum_canis","Uncinocarpus_reesii","Trichophyton_rubrum","Basipetospora_chlamydospora","Coccidioides_posadasii","Paracoccidioides_brasiliensis","Trichoderma_reesei","Coccidioides_immitis","Histoplasma_capsulatum","Talaromyces_occitanis","Talaromyces_marneffei")
      }
    })

  ## display proper citation based on associated manuscript
  output$FUNGIcitationText <- renderText({
      if (input$FUNGIphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
        paste("If you use this subtree, please cite: Steenwyk et al. 2019, mBio: 10.1128/mBio.00925-19")
      } else if (input$FUNGIphyloSelect == "Saccharomycotina, 86 taxa - Shen et al. 2016") {
        paste("If you use this subtree, please cite: Shen et al. 2016, G3. doi: 10.1534/g3.117.040105")
      } else if (input$FUNGIphyloSelect == "Saccharomycotina, 332 taxa - Shen et al. 2018") {
        paste("If you use this subtree, please cite: Shen et al. 2018, Cell. doi: 10.1016/j.cell.2018.10.023")
      } else if (input$FUNGIphyloSelect == "Saccharomyces cerevisiae, 1,011 strains - Peter et al. 2018") {
        paste("If you use this subtree, please cite: Peter et al. 2018, Nature. doi: 10.1038/s41586-018-0030-5")
      } else if (input$FUNGIphyloSelect == "Cryptococcus neoformans, 387 strains - Desjardins et al. 2017") {
        paste("If you use this subtree, please cite: Desjardins et al. 2017, Genome Research. doi: 10.1101/gr.218727.116")
      } else if (input$FUNGIphyloSelect == "Fungi, 214 taxa - James et al. 2006") {
        paste("If you use this subtree, please cite: James et al. 2006, Nature. doi: 10.1038/nature05110")
      } else if (input$FUNGIphyloSelect == "Agaricomycetes, 5,284 taxa - Varga et al. 2019") {
        paste("If you use this subtree, please cite: Varga et al. 2019, Nature Ecology and Evolution. doi: 10.1038/s41559-019-0834-1")
      } else if (input$FUNGIphyloSelect == "Fungi, 60 taxa - Nagy et al. 2014") {
        paste("If you use this subtree, please cite: Nagy et al. 2014, Nature Communications. doi: 10.1038/ncomms5471")
      } else if (input$FUNGIphyloSelect == "Ascomycota, 1,113 taxa - Shen et al. 2020") {
        paste("If you use this subtree, please cite: Shen et al. 2020, bioRxiv. doi: 10.1101/2020.05.11.088658v1")
      } else 
        paste("If you use this subtree, please cite: Steenwyk et al. 2018, bioRxiv")
    })

  ## display table of taxa names
  FUNGItipNames <- eventReactive(input$FUNGIgo, {
      a<-data.frame(FUNGItree()$tip.label)
      # replace column name to "full list of taxa"
      colnames(a)[1]<-"full list of taxa for possible subtree"
      # return to df_subset
      return(a)
    })
  output$FUNGItaxaTable <- renderTable(FUNGItipNames())
  
  ## function to create plot
  output$FUNGIphyloPlot <- renderPlot({
    # root tree
    tree<-root(FUNGItree(), outgroup = FUNGIoutgroup.labels(), resolve.root = TRUE) 
    # drop outgroup tips not in ingroup.labels
    ingroup.labels<-as.vector(FUNGIdata()$V1)
    outgroup.labels<-setdiff(FUNGIoutgroup.labels(),ingroup.labels)
    tree<-drop.tip(tree, outgroup.labels)
    # prune taxa not of interest
    pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
    if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
    # plot tree
    p<-try(plotTree(pruned.tree))
    if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
    p
    add.scale.bar(cex = 0.7, font = 2, col = "black")
  })
  
  ## save pdf
  output$FUNGITreePlot<- downloadHandler(
    #Specify The File Name 
    filename = function() {
      paste("treehouse-",Sys.Date(),".pdf",sep= "")},
    content = function(file){
      # open the pdf
      pdf(file)
      # root tree
      tree<-root(FUNGItree(), outgroup = FUNGIoutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(FUNGIdata()$V1)
      outgroup.labels<-setdiff(FUNGIoutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      add.scale.bar(cex = 0.7, font = 2, col = "black")
      dev.off()
    }
  )
  
  ## write treefile
  output$FUNGINewick<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      # root tree
      tree<-root(FUNGItree(), outgroup = FUNGIoutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(FUNGIdata()$V1)
      outgroup.labels<-setdiff(FUNGIoutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      # write tree file out
      write.tree(pruned.tree, file=file)
    }
  )

  ## write treefile
  output$FUNGINewickNOBL<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      # root tree
      tree<-root(FUNGItree(), outgroup = FUNGIoutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(FUNGIdata()$V1)
      outgroup.labels<-setdiff(FUNGIoutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      # write tree file out
      prune.tree$edge.length<-NULL
      write.tree(pruned.tree, file=file)
    }
  )

  ##############
  ### ANIMAL ###
  ##############

  ## read in file reactively
  ANIMALdata <- eventReactive(input$ANIMALgo, { 
    req(input$ANIMALfile)
    inFile <- input$ANIMALfile
    taxa.list<-read.table(inFile$datapath)
    return(taxa.list)
    })

  ## read in tree based on selected tree
  ANIMALtree <- eventReactive(input$ANIMALgo, {
    if (input$ANIMALphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
      ANIMALtree <- read.tree("./Data/Aspergillaceae_fig1_Steenwyk_etal_2018.tre")
    } else if (input$ANIMALphyloSelect == "Metazoans, 36 taxa - Borowiec et al. 2015") {
      ANIMALtree <- read.tree("./Data/Metazoans_fig3_Borowiec_etal_2015.tre")  
    } else if (input$ANIMALphyloSelect == "Birds, 198 taxa - Prum et al. 2015") {
      ANIMALtree <- read.tree("./Data/Birds_fig1_Prum_etal_2015.tre")   
    } else if (input$ANIMALphyloSelect == "Vertebrates, 58 taxa - Chen et al. 2015") {
      ANIMALtree <- read.nexus("./Data/Vertebrates_fig1_Chen_etal_2015.tre")  
    } else if (input$ANIMALphyloSelect == "Metazoans, 70 taxa - Whelan et al. 2015" ) {
      ANIMALtree <- read.tree("./Data/Metazoans_fig3_Whelan_etal_2015.tre")
    } else if (input$ANIMALphyloSelect == "Birds, 48 taxa - Jarvis et al. 2014" ) {
      ANIMALtree <- read.tree("./Data/Birds_fig1_Jarvis_etal_2014.tre")
    } else if (input$ANIMALphyloSelect == "Mammals, 36 taxa - Tarver et al. 2016" ) {
      ANIMALtree <- read.tree("./Data/Mammals_fig2_Tarver_etal_2016.tre")
    } else if (input$ANIMALphyloSelect == "Insects, 144 taxa - Misof et al. 2014" ) {
      ANIMALtree <- read.tree("./Data/Insects_fig1_Misof_etal_2014.tre")
    } else if (input$ANIMALphyloSelect == "Mammals, 37 taxa - Song et al. 2016" ) {
      ANIMALtree <- read.tree("./Data/Mammals_fig1_Song_etal_2012.tre")
    } else if (input$ANIMALphyloSelect == "Worms, 100 taxa - Struck et al. 2015" ) {
      ANIMALtree <- read.tree("./Data/Worms_fig1_Struck_etal_2015.tre")
    } else 
      ANIMALtree <- read.tree("./Data/Aspergillaceae_fig1_Steenwyk_etal_2018.tre")
  })

  ## select outgroup labels based on selected tree
  ANIMALoutgroup.labels <- eventReactive(input$ANIMALgo, {input$ANIMALphyloSelect
    if (input$ANIMALphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
      ANIMALoutgroup.labels<-c("Neurospora_crassa","Microsporum_canis","Uncinocarpus_reesii","Trichophyton_rubrum","Basipetospora_chlamydospora","Coccidioides_posadasii","Paracoccidioides_brasiliensis","Trichoderma_reesei","Coccidioides_immitis","Histoplasma_capsulatum","Talaromyces_occitanis","Talaromyces_marneffei")
      }
      else if (input$ANIMALphyloSelect == "Metazoans, 36 taxa - Borowiec et al. 2015") {
      ANIMALoutgroup.labels<-c("Monosiga", "Salpingoeca")
      }
      else if (input$ANIMALphyloSelect == "Birds, 198 taxa - Prum et al. 2015") {
      ANIMALoutgroup.labels<-c("I0461_HERP_15451_Alligatoridae_Caiman_croccodilus", "I0460_HERP_14722_Crocodylidae_Crocodylus_porosus")
      }
      else if (input$ANIMALphyloSelect == "Vertebrates, 58 taxa - Chen et al. 2015") {
      ANIMALoutgroup.labels<-c("Cmi", "Sca", "Ler")
      }
      else if (input$ANIMALphyloSelect == "Metazoans, 70 taxa - Whelan et al. 2015") {
      ANIMALoutgroup.labels<-c("Allomyces_macrogynus","Rhizopus_oryzae","Mortierella_verticillata","Spizellomyces_punctatus")
      }
      else if (input$ANIMALphyloSelect == "Birds, 48 taxa - Jarvis et al. 2014") {
      ANIMALoutgroup.labels<-c("ANAPL","GALGA","MELGA","TINMA","STRCA")
      }
      else if (input$ANIMALphyloSelect == "Insects, 144 taxa - Misof et al. 2014") {
      ANIMALoutgroup.labels<-c("IXODES_S")
      }
      else if (input$ANIMALphyloSelect == "Mammals, 36 taxa - Tarver et al. 2016") {
      ANIMALoutgroup.labels<-c("P001_Platypus")
      }
      else if (input$ANIMALphyloSelect == "Mammals, 37 taxa - Song et al. 2016") {
      ANIMALoutgroup.labels<-c("Gal","Orn")
      }
      else if (input$ANIMALphyloSelect == "Worms, 100 taxa - Struck et al. 2015") {
      ANIMALoutgroup.labels<-c("Crassostrea_gigas","Lottia_gigantea","Euprymna_scolopes","Hanleya_sp")
      }
      else {
      ANIMALoutgroup.labels<-c("Neurospora_crassa","Microsporum_canis","Uncinocarpus_reesii","Trichophyton_rubrum","Basipetospora_chlamydospora","Coccidioides_posadasii","Paracoccidioides_brasiliensis","Trichoderma_reesei","Coccidioides_immitis","Histoplasma_capsulatum","Talaromyces_occitanis","Talaromyces_marneffei")
      }
    })

  ## display proper citation based on associated manuscript
  output$ANIMALcitationText <- renderText({
      if (input$ANIMALphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
        paste("If you use this subtree, please cite: Steenwyk et al. 2018, bioRxiv. 10.1101/370429")
      } else if (input$ANIMALphyloSelect == "Metazoans, 36 taxa - Borowiec et al. 2015") {
        paste("If you use this subtree, please cite: Borowiec et al. 2015, BMC Genomics. doi: 10.1186/s12864-015-2146-4")
      } else if (input$ANIMALphyloSelect == "Birds, 198 taxa - Prum et al. 2015") {
        paste("If you use this subtree, please cite: Prum et al. 2015, Nature doi: 10.1038/nature15697")
      } else if (input$ANIMALphyloSelect == "Vertebrates, 58 taxa - Chen et al. 2015") {
        paste("If you use this subtree, please cite: Chen et al. 2015, Systematic Biology doi: 10.1093/sysbio/syv059")
      } else if (input$ANIMALphyloSelect == "Metazoans, 70 taxa - Whelan et al. 2015") {
        paste("If you use this subtree, please cite: Whelan et al. 2015, Proceedings of the National Academy of Sciences of the USA doi: 10.1073/pnas.1503453112") 
      } else if (input$ANIMALphyloSelect == "Birds, 48 taxa - Jarvis et al. 2014") {
        paste("If you use this subtree, please cite: Jarvis et al. 2014, Science doi: 10.1126/science.1253451")
      } else if (input$ANIMALphyloSelect == "Mammals, 36 taxa - Tarver et al. 2016") {
        paste("If you use this subtree, please cite: Tarver et al. 2016, Genome Biology and Evolution doi: 10.1093/gbe/evv261 and Zhou et al. 2017, Molecular Biology and Evolution. doi: 10.1093/molbev/msx302. Phylogeny with branch lengths was obtained from Zhou et al. 2017, MBE.")
      } else if (input$ANIMALphyloSelect == "Insects, 144 taxa - Misof et al. 2014") {
        paste("If you use this subtree, please cite: Misof et al. 2014, Science doi: 10.1126/science.1257570 and Zhou et al. 2017, Molecular Biology and Evolution. doi: 10.1093/molbev/msx302. Phylogeny with branch lengths was obtained from Zhou et al. 2017, MBE.")
      } else if (input$ANIMALphyloSelect == "Mammals, 37 taxa - Song et al. 2016") {
        paste("If you use this subtree, please cite: Song et al. 2012, Proceedings of the National Academy of Sciences of the USA doi: 10.1073/pnas.1211733109 and Zhou et al. 2017, Molecular Biology and Evolution. doi: 10.1093/molbev/msx302. Phylogeny with branch lengths was obtained from Zhou et al. 2017, MBE.")
      } else if (input$ANIMALphyloSelect == "Worms, 100 taxa - Struck et al. 2015") {
        paste("If you use this subtree, please cite: Struck et al. 2015, Current Biology doi: 10.1016/j.cub.2015.06.007 and Zhou et al. 2017, Molecular Biology and Evolution. doi: 10.1093/molbev/msx302. Phylogeny with branch lengths was obtained from Zhou et al. 2017, MBE.")
      } else 
        paste("If you use this subtree, please cite: Steenwyk et al. 2018, bioRxiv")
    })

  ## display table of taxa names
  ANIMALtipNames <- eventReactive(input$ANIMALgo, {
      a<-data.frame(ANIMALtree()$tip.label)
      # replace column name to "full list of taxa"
      colnames(a)[1]<-"full list of taxa for possible subtree"
      # return to df_subset
      return(a)
    })
  output$ANIMALtaxaTable <- renderTable(ANIMALtipNames())
  
  ## function to create plot
  output$ANIMALphyloPlot <- renderPlot({
    # root tree
    tree<-root(ANIMALtree(), outgroup = ANIMALoutgroup.labels(), resolve.root = TRUE) 
    # drop outgroup tips not in ingroup.labels
    ingroup.labels<-as.vector(ANIMALdata()$V1)
    outgroup.labels<-setdiff(ANIMALoutgroup.labels(),ingroup.labels)
    tree<-drop.tip(tree, outgroup.labels)
    # prune taxa not of interest
    pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
    if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
    # plot tree
    p<-try(plotTree(pruned.tree))
    if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
    p
    add.scale.bar(cex = 0.7, font = 2, col = "black")
  })
  
  ## save pdf
  output$ANIMALTreePlot<- downloadHandler(
    #Specify The File Name 
    filename = function() {
      paste("treehouse-",Sys.Date(),".pdf",sep= "")},
    content = function(file){
      # open the pdf
      pdf(file)
      # root tree
      tree<-root(ANIMALtree(), outgroup = ANIMALoutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(ANIMALdata()$V1)
      outgroup.labels<-setdiff(ANIMALoutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      add.scale.bar(cex = 0.7, font = 2, col = "black")
      dev.off()
    }
  )
  
  ## write treefile
  output$ANIMALNewick<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      # root tree
      tree<-root(ANIMALtree(), outgroup = ANIMALoutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(ANIMALdata()$V1)
      outgroup.labels<-setdiff(ANIMALoutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      # write tree file out
      write.tree(pruned.tree, file=file)
    }
  )

  ## write treefile
  output$ANIMALNewickNOBL<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      # root tree
      tree<-root(ANIMALtree(), outgroup = ANIMALoutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(ANIMALdata()$V1)
      outgroup.labels<-setdiff(ANIMALoutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      pruned.tree$edge.length<-NULL
      # write tree file out
      write.tree(pruned.tree, file=file)
    }
  )

  #############
  ### PLANT ###
  #############

  ## read in file reactively
  PLANTdata <- eventReactive(input$PLANTgo, { 
    req(input$PLANTfile)
    inFile <- input$PLANTfile
    taxa.list<-read.table(inFile$datapath)
    return(taxa.list)
    })

  ## read in tree based on selected tree
  PLANTtree <- eventReactive(input$PLANTgo, {
    if (input$PLANTphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
      PLANTtree <- read.tree("./Data/Aspergillaceae_fig1_Steenwyk_etal_2018.tre")
    } else if (input$PLANTphyloSelect == "Flowering plants, 45 taxa - Xi et al. 2014") {
      PLANTtree <- read.tree("./Data/Flowering_plants_fig2_Xi_etal_2014.tre")  
    } else if (input$PLANTphyloSelect == "Caryophyllales, 95 taxa - Yang et al. 2015") {
      PLANTtree <- read.tree("./Data/Caryophyllales_fig3_Yang_etal_2015.tre")  
    } else if (input$PLANTphyloSelect == "Land plants, 103 taxa - Wickett et al. 2014") {
      PLANTtree <- read.tree("./Data/Land_plants_fig2_Wickett_etal_2014.tre")
    } else 
      PLANTtree <- read.tree("./Data/Aspergillaceae_fig1_Steenwyk_etal_2018.tre")
  })

  ## select outgroup labels based on selected tree
  PLANToutgroup.labels <- eventReactive(input$PLANTgo, {input$PLANTphyloSelect
    if (input$PLANTphyloSelect == "Flowering plants, 45 taxa - Xi et al. 2014") {
      PLANToutgroup.labels<-c("Picea","Pinus","Zamia","Selaginella")
      }
      else if (input$PLANTphyloSelect == "Caryophyllales, 95 taxa - Yang et al. 2015") {
      PLANToutgroup.labels<-c("Rcom","Ptri","Pper","Mdom","Fves","Csat","Pvul","Gmax","Mtru","Egra","Vvin","Ccle","Csin","Tcac","Grai","Cpap","Atha","Alyr","Crub","Brap","Thal","Lusi","Mesc")
      }
      else if (input$PLANTphyloSelect == "Land plants, 103 taxa - Wickett et al. 2014") {
      PLANToutgroup.labels<-c("Uronema_sp", "Monomastix_opisthostigma","Nephroselmis_pyriformis","Pyramimonas_parkeae")
      }
      else {
      PLANToutgroup.labels<-c("Picea","Pinus","Zamia","Selaginella")
      }
    })

  ## display proper citation based on associated manuscript
  output$PLANTcitationText <- renderText({
      if (input$PLANTphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
        paste("If you use this subtree, please cite: Steenwyk et al. 2018, bioRxiv. 10.1101/370429")
      } else if (input$PLANTphyloSelect == "Flowering plants, 45 taxa - Xi et al. 2014") {
        paste("If you use this subtree, please cite: Xi et al. 2014, Systematic Biology. doi: 10.1093/sysbio/syu055 and Zhou et al. 2017, Molecular Biology and Evolution. doi: 10.1093/molbev/msx302. Phylogeny with branch lengths was obtained from Zhou et al. 2017, MBE.")
      } else if (input$PLANTphyloSelect == "Caryophyllales, 95 taxa - Yang et al. 2015") {
        paste("If you use this subtree, please cite: Yang et al. 2015, Molecular Biology and Evolution. doi: 10.1093/molbev/msv081")
      } else if (input$PLANTphyloSelect == "Land plants, 103 taxa - Wickett et al. 2014") {
        paste("If you use this subtree, please cite: Wickett et al. 2014, Proceedings of the National Academy of Sciences of the USA. doi: 10.1073/pnas.1323926111")
      } else 
        paste("If you use this subtree, please cite: Steenwyk et al. 2018, bioRxiv")
    })

  ## display table of taxa names
  PLANTtipNames <- eventReactive(input$PLANTgo, {
      a<-data.frame(PLANTtree()$tip.label)
      # replace column name to "full list of taxa"
      colnames(a)[1]<-"full list of taxa for possible subtree"
      # return to df_subset
      return(a)
    })
  output$PLANTtaxaTable <- renderTable(PLANTtipNames())
  
  ## function to create plot
  output$PLANTphyloPlot <- renderPlot({
    # root tree
    tree<-root(PLANTtree(), outgroup = PLANToutgroup.labels(), resolve.root = TRUE) 
    # drop outgroup tips not in ingroup.labels
    ingroup.labels<-as.vector(PLANTdata()$V1)
    outgroup.labels<-setdiff(PLANToutgroup.labels(),ingroup.labels)
    tree<-drop.tip(tree, outgroup.labels)
    # prune taxa not of interest
    pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
    if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
    # plot tree
    p<-try(plotTree(pruned.tree))
    if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
    p
    add.scale.bar(cex = 0.7, font = 2, col = "black")
  })
  
  ## save pdf
  output$PLANTTreePlot<- downloadHandler(
    #Specify The File Name 
    filename = function() {
      paste("treehouse-",Sys.Date(),".pdf",sep= "")},
    content = function(file){
      # open the pdf
      pdf(file)
      # root tree
      tree<-root(PLANTtree(), outgroup = PLANToutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(PLANTdata()$V1)
      outgroup.labels<-setdiff(PLANToutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      add.scale.bar(cex = 0.7, font = 2, col = "black")
      dev.off()
    }
  )
  
  ## write treefile
  output$PLANTNewick<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      # root tree
      tree<-root(PLANTtree(), outgroup = PLANToutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(PLANTdata()$V1)
      outgroup.labels<-setdiff(PLANToutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      # write tree file out
      write.tree(pruned.tree, file=file)
    }
  )

  ## write treefile
  output$PLANTNewickNOBL<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      # root tree
      tree<-root(PLANTtree(), outgroup = PLANToutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(PLANTdata()$V1)
      outgroup.labels<-setdiff(PLANToutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      # write tree file out
      pruned.tree$edge.length<-NULL
      write.tree(pruned.tree, file=file)
    }
  )

  ####################
  ### TREE OF LIFE ###
  ####################

  ## read in file reactively
  TOLdata <- eventReactive(input$TOLgo, { 
    req(input$TOLfile)
    inFile <- input$TOLfile
    taxa.list<-read.table(inFile$datapath)
    return(taxa.list)
    })

  ## read in tree based on selected tree
  TOLtree <- eventReactive(input$TOLgo, {
    if (input$TOLphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
      TOLtree <- read.tree("./Data/Aspergillaceae_fig1_Steenwyk_etal_2018.tre")
    } else if (input$TOLphyloSelect == "Tree of life, 3,083 taxa - Hug et al. 2016") {
      TOLtree <- read.tree("./Data/Tree_of_Life_fig1_Hug_etal_2016.tre") 
    } else 
      TOLtree <- read.tree("./Data/Aspergillaceae_fig1_Steenwyk_etal_2018.tre")
  })

  ## select outgroup labels based on selected tree
  TOLoutgroup.labels <- eventReactive(input$TOLgo, {input$TOLphyloSelect
    if (input$TOLphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
      TOLoutgroup.labels<-c("Neurospora_crassa","Microsporum_canis","Uncinocarpus_reesii","Trichophyton_rubrum","Basipetospora_chlamydospora","Coccidioides_posadasii","Paracoccidioides_brasiliensis","Trichoderma_reesei","Coccidioides_immitis","Histoplasma_capsulatum","Talaromyces_occitanis","Talaromyces_marneffei")
      }
      else if (input$TOLphyloSelect == "Tree of life, 3,083 taxa - Hug et al. 2016") {
      TOLoutgroup.labels<-c("Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Lelliottia_amnigena_CHS_78","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Leclercia_adecarboxylata_Leclerc_1783_ATCC_23216","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Kluyvera_ascorbata_ATCC_33433","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Citrobacter_rodentium_ICC168","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Salmonella_enterica_Enterica_sv._Heidelberg_41578","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Escherichia_coli_K12__W3110","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Shigella_flexneri_2003036","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Yokenella_regensburgei_ATCC_43003","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Cronobacter_sakazakii_CMCC_45402","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Kosakonia_radicincitans_UMEnt0112","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Trabulsiella_guamensis_ATCC_49490","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Enterobacter_cloacae_SCF1","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Raoultella_ornithinolytica_B6","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Klebsiella_oxytoca_HKOPL1","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Buttiauxella_agrestis_MCE","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Cedecea_davisae_DSM_4568","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Tatumella_ptyseos_ATCC_33301","Bacteria_Proteobacteria_Gammaproteobacteria_Pseudomonadales_Pseudomonadaceae_Pseudomonas_flectens_ATCC_12775","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Pantoea_ananatis_LMG_5342","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Erwinia_amylovora_CFBP1430","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Pectobacterium_carotovorum_carotovorum_PCC21","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Brenneria_salicis_ATCC_15712","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Lonsdalea_quercina_quercina_NCCB_100489","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Dickeya_dadantii_Ech703","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Wigglesworthia_glossinidia_endosymbiont_of_Glossina_brevipalpis","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Candidatus_Riesia_pediculicola_USDA","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_unclassified_Enterobacteriaceae_Candidatus_Blochmannia_floridanus","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Buchnera_Buchnera_aphidicola_str._APS_Acyrthosiphon_pisum","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_unclassified_Enterobacteriaceae_Candidatus_Hamiltonella_defensa_5AT_Acyrthosiphon_pisum","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Halyomorpha_halys_symbiont","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Thorsellia_anophelis_DSM_18579","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Sodalis_glossinidius_morsitans","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Candidatus_Moranella_endobia_PCIT","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_unclassified_Enterobacteriaceae_Candidatus_Regiella_insecticola_LSR1_genomic_scaffold_Scaffold1","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Yersinia_pestis_Nepal516","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Serratia_fonticola_RB_25","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Ewingella_americana_C.024_ATCC_33852","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Rahnella_aquatilis_HX2","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Hafnia_alvei_FB1","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Edwardsiella_tarda_C07_087","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Arsenophonus_nasoniae_DSM_15247","Bacteria_Proteobacteria_Gammaproteobacteria_Enterobacteriales_Enterobacteriaceae_Providencia_stuartii_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roteobacteria_Burkholderiales_Sutterellaceae_Sutterella_wadsworthensis_HGA0223","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Sutterellaceae_Parasutterella_Parasutterella_excrementihominis_YIT_11859_P_excrementihominisYIT11859_1.0_Cont110.1_whole_genome_shotgun","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Burkholderiaceae_Limnobacter_sp._MED105_unfinished_sequence","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Brackiella_oedipodis_DSM_13743","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Oligella_ureolytica_DSM_18253","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Pelistega_sp._HM_7","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Taylorella_asinigenitalis_MCE3","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Basilea_psittacipulmonis_DSM_24701","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Tetrathiobacter_kashmirensis_WT001","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Achromobacter_xylosoxidans_NBRC_15126_ATCC_27061","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Bordetella_bronchiseptica_RB50","Bacteria_Proteobacteria_Betaproteobacteria_unclassified_Betaproteobacteria_Candidatus_Kinetoplastibacterium_oncopeltii_TCC290E","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Pusillimonas_sp._T7_7","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Alcaligenes_faecalis_phenolicus_DSM_16503","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Burkholderiaceae_Lautropia_mirabilis_ATCC_51599_contig00020","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Oxalobacteraceae_Duganella_zoogloeoides_ATCC_25935","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Zoogloea_ramigera_ATCC_19544","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Oxalobacteraceae_Massilia_alkalitolerans_DSM_17462","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Oxalobacteraceae_Janthinobacterium_sp._Marseille","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Oxalobacteraceae_Herminiimonas_arsenicoxydans","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Oxalobacteraceae_Collimonas_fungivorans_Ter331","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Oxalobacteraceae_Herbaspirillum_seropedicae_SmR1","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Oxalobacteraceae_Oxalobacter_formigenes_OXCC13_genomic_scaffold_supercont1.1","Bacteria_Proteobacteria_Betaproteobacteria_unclassified_Betaproteobacteria_Candidatus_Profftella_armatura_syncytium_symbiont_of_Diaphorina_citri","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Burkholderiaceae_Ralstonia_solanacearum_GMI1000","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Burkholderiaceae_Ralstonia_eutropha_JMP134","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Burkholderiaceae_Polynucleobacter_necessarius_asymbioticus_MWH_MoK4_closed_genome","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Burkholderiaceae_Glomeribacter_sp._1016415","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Burkholderiaceae_Burkholderia_cenocepacia_AU_1054","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Burkholderiaceae_Pandoraea_pnomenusa_RB38","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Alcaligenaceae_Derxia_gummosa_DSM_723","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Dechlorobacter_hydrogenophilus_LT_1","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Dechloromonas_aromatica_RCB","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Azonexus_hydrophilus_DSM_23864","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Azovibrio_restrictus_DSM_23866","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Dechlorosoma_suillum_PS","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Propionivibrio_dicarboxylicus_DSM_5885","Bacteria_Proteobacteria_Betaproteobacteria_unclassified_Betaproteobacteria_Candidatus_Accumulibacter_phosphatis_clade_IIA_str._UW_1","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Aromatoleum_aromaticum_EbN1","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Azoarcus_sp._KH32C","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Thauera_sp._MZ1T","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Uliginosibacterium_gangwonense_DSM_18521","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_CG2_30_FULL_Betaproteobacteria_68_42","Bacteria_Proteobacteria_Betaproteobacteria_Hydrogenophilales_Hydrogenophilaceae_Tepidiphilus_margaritifer_DSM_15129","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_GWA2_Rhodocyclales_65_20","Bacteria_Proteobacteria_Betaproteobacteria_Rhodocyclales_Rhodocyclaceae_Methyloversatilis_universalis_EHg5","Bacteria_Proteobacteria_Betaproteobacteria_uncultured_SG8_41","Bacteria_Proteobacteria_Betaproteobacteria_uncultured_SG8_39","Bacteria_Proteobacteria_Betaproteobacteria_uncultured_SG8_40","Bacteria_Proteobacteria_Betaproteobacteria_Gallionellales_Gallionellaceae_Ferriphaselus_sp._R_1","Bacteria_Proteobacteria_Betaproteobacteria_Gallionellales_Gallionellaceae_Gallionella_capsiferriformans_ES_2","Bacteria_Proteobacteria_Betaproteobacteria_Gallionellales_Gallionellaceae_Sideroxydans_lithotrophicus_ES_1","Bacteria_Proteobacteria_Betaproteobacteria_Nitrosomonadales_Nitrosomonadaceae_Nitrosospira_multiformis_ATCC_25196","Bacteria_Proteobacteria_Betaproteobacteria_Nitrosomonadales_Nitrosomonadaceae_Nitrosomonas_europaea_ATCC_19718","Bacteria_Proteobacteria_Betaproteobacteria_Hydrogenophilales_Hydrogenophilaceae_Thiobacillus_denitrificans_ATCC_25259","Bacteria_Proteobacteria_Betaproteobacteria_Hydrogenophilales_GWE1_Thiobacillus_62_9","Bacteria_Proteobacteria_Betaproteobacteria_Hydrogenophilales_Hydrogenophilaceae_CG1_02_SUB10_Hydrogenophilaceae_62_390","Bacteria_Proteobacteria_Betaproteobacteria_Hydrogenophilales_Hydrogenophilaceae_Sulfuricella_denitrificans_skB26","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Simonsiella_muelleri_ATCC_29453","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Kingella_kingae_PYKK081","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Alysiella_crassa_DSM_2578","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Conchiformibius_steedae_DSM_2580","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Eikenella_corrodens_ATCC_23834","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Neisseria_gonorrhoeae_FA_1090","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Stenoxybacter_acetivorans_DSM_19021","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Snodgrassella_alvi_wkB2","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Chromobacterium_group_Vitreoscilla_stercoraria_DSM_513","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Chromobacteriaceae_Lutiella_nitroferrum_2002_unfinished_sequence","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Paludibacterium_yongneupense_DSM_18731","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Chromobacterium_group_Chromobacterium_violaceum_ATCC_12472","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Microvirgula_aerodenitrificans_DSM_15089","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Laribacter_hongkongensis_HLHK9","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Deefgea_rivuli_DSM_18356","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Formivibrio_citricus_DSM_6150","Bacteria_Proteobacteria_Betaproteobacteria_Burkholderiales_Burkholderiaceae_Chitinimonas_koreensis_DSM_17726","Bacteria_Proteobacteria_Betaproteobacteria_Neisseriales_Neisseriaceae_Leeia_oryzae_DSM_17879","Bacteria_Proteobacteria_Betaproteobacteria_Methylophilales_Methylophilaceae_Methylophilus_methylotrophus_ATCC_53528","Bacteria_Proteobacteria_Betaproteobacteria_Methylophilales_Methylophilaceae_Methylotenera_sp._301","Bacteria_Proteobacteria_Betaproteobacteria_Methylophilales_Methylophilaceae_Methylovorus_sp._SIP3_4","Bacteria_Proteobacteria_Betaproteobacteria_Methylophilales_Methylophilaceae_Methylobacillus_flagellatus_KT","Bacteria_Proteobacteria_Acidithiobacillia_Acidithiobacillales_Thermithiobacillaceae_Thermithiobacillus_tepidarius_DSM_3134","Bacteria_Proteobacteria_Acidithiobacillia_Acidithiobacillales_Acidithiobacillaceae_Acidithiobacillus_ferrivorans_SS3","Bacteria_Proteobacteria_Gammaproteobacteria_unclassified_Gammaproteobacteria_Thiohalorhabdus_denitrificans_HL19","Bacteria_Proteobacteria_Zetaproteobacteria_zeta_proteobacterium_SCGC_AB_137_J06","Bacteria_Proteobacteria_Zetaproteobacteria_zeta_proteobacterium_SCGC_AB_133_G06","Bacteria_Proteobacteria_Zetaproteobacteria_Mariprofundales_Mariprofundaceae_Mariprofundus_ferrooxydans_M34","Bacteria_Proteobacteria_Zetaproteobacteria_Mariprofundales_Mariprofundaceae_Mariprofundus_sp._EKF_M39","Bacteria_Proteobacteria_Zetaproteobacteria_zeta_proteobacterium_SCGC_AB_137_L23","Bacteria_Proteobacteria_Zetaproteobacteria_zeta_proteobacterium_SCGC_AB_137_C09","Bacteria_Proteobacteria_Zetaproteobacteria_zeta_proteobacterium_SCGC_AB_137_I08","Bacteria_Proteobacteria_Zetaproteobacteria_zeta_proteobacterium_SCGC_AB_133_C04","Bacteria_Proteobacteria_Zetaproteobacteria_Zetaproteobacteria_bacterium_TAG_1","Bacteria_Proteobacteria_Zetaproteobacteria_zeta_proteobacterium_SCGC_AC_673_C02","Bacteria_Proteobacteria_Zetaproteobacteria_zeta_proteobacterium_SCGC_AC_673_M07","Bacteria_Proteoba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_Microgenomates_OP11_Curtissbacteria_RIFCSPLOWO2_02_FULL_OP11_Curtissbacteria_40_11","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RBG_13_OP11_Curtissbacteria_35_7","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RIFCSPLOWO2_01_FULL_OP11_Curtissbacteria_38_11b","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RIFCSPLOWO2_01_FULL_OP11_Curtissbacteria_42_26","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RIFCSPLOWO2_01_FULL_OP11_Curtissbacteria_41_18","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_Microgenomates_bacterium_SCGC_AAA011_L6_Dusel_001_266","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_GWA1_OP11_40_9_partial","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_GWA1_OP11_40_16_partial","Bacteria_CPR_Microgenomates_OP11_RBG_13_OP11_40_7","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RIFCSPHIGHO2_12_FULL_OP11_Curtissbacteria_38_9b","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RIFCSPHIGHO2_12_FULL_OP11_Curtissbacteria_41_17","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_GWA1_OP11_40_24_partial","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RIFCSPHIGHO2_02_FULL_OP11_Curtissbacteria_42_15","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RIFCSPLOWO2_02_OP11_Curtissbacteria_41_11","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_GWA1_OP11_40_47","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RIFCSPHIGHO2_01_FULL_OP11_Curtissbacteria_41_44","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RIFCSPHIGHO2_01_FULL_OP11_Curtissbacteria_41_11","Bacteria_CPR_Microgenomates_OP11_Curtissbacteria_RBG_16_OP11_Curtissbacteria_39_7","Bacteria_CPR_Microgenomates_OP11_RBG_16_OP11_43_9","Bacteria_CPR_Microgenomates_OP11_RBG_19FT_COMBO_OP11_43_10","Bacteria_CPR_Microgenomates_OP11_RBG_13_OP11_40_15","Bacteria_CPR_Microgenomates_OP11_RBG_16_OP11_44_10","Bacteria_CPR_Microgenomates_OP11_GWB1_OP11_45_5","Bacteria_CPR_Microgenomates_OP11_RIFCSPLOWO2_01_FULL_OP11_41_12","Bacteria_CPR_Microgenomates_OP11_RBG_16_OP11_39_9b","Bacteria_CPR_Microgenomates_OP11_RIFCSPHIGHO2_12_FULL_OP11_45_10","Bacteria_CPR_Microgenomates_OP11_RBG_13_OP11_40_7b","Bacteria_CPR_Microgenomates_OP11_RIFCSPLOWO2_01_FULL_OP11_43_14","Bacteria_CPR_WWE3_RIFOXYD1_FULL_WWE3_43_17","Bacteria_CPR_WWE3_GWB1_WWE3_42_6","Bacteria_CPR_WWE3_RIFOXYC1_FULL_WWE3_42_17","Bacteria_CPR_WWE3_RIFOXYD2_FULL_WWE3_43_10","Bacteria_CPR_WWE3_RAAC2_WWE3_complete","Bacteria_CPR_WWE3_RIFOXYA2_FULL_WWE3_46_9","Bacteria_CPR_WWE3_RIFOXYD1_FULL_WWE3_39_9","Bacteria_CPR_WWE3_RBG_13_WWE3_37_7","Bacteria_CPR_WWE3_RIFCSPLOWO2_01_FULL_WWE3_37_15","Bacteria_CPR_WWE3_RBG_16_WWE3_37_10","Bacteria_CPR_WWE3_RIFCSPHIGHO2_12_FULL_WWE3_38_15","Bacteria_CPR_WWE3_GWB1_WWE3_41_6","Bacteria_CPR_WWE3_RBG_19FT_COMBO_WWE3_34_6","Bacteria_CPR_WWE3_GWA2_WWE3_46_9","Bacteria_CPR_WWE3_GWA2_WWE3_44_16","Bacteria_CPR_WWE3_RIFCSPHIGHO2_01_FULL_WWE3_42_13","Bacteria_CPR_WWE3_RIFCSPLOWO2_12_FULL_WWE3_36_10","Bacteria_CPR_WWE3_RIFCSPHIGHO2_01_FULL_WWE3_40_23","Bacteria_CPR_WWE3_CG2_30_FULL_WWE3_related_40_12","Bacteria_CPR_WWE3_RIFCSPHIGHO2_01_FULL_WWE3_35_17","Bacteria_CPR_WWE3_RIFCSPLOWO2_01_FULL_WWE3_39_13","Bacteria_CPR_WWE3_RIFCSPLOWO2_01_FULL_WWE3_42_11","Bacteria_CPR_WWE3_CSP1_7","Bacteria_CPR_WWE3_RIFCSPLOWO2_01_FULL_WWE3_53_14","Bacteria_CPR_WWE3_RBG_19FT_COMBO_WWE3_53_11","Bacteria_CPR_WWE3_RIFCSPHIGHO2_01_FULL_WWE3_48_15","Bacteria_CPR_CPR3_CG1_02_FULL_CPR3_42_9","Bacteria_CPR_CPR3_GWF2_CPR3_35_18","Bacteria_CPR_CPR1_GWA2_CPR1_42_17","Bacteria_CPR_Dojkabacteria_WS6_GWE1_WS6_34_7","Bacteria_CPR_Dojkabacteria_WS6_RIFOXYB1_FULL_WS6_33_14","Bacteria_CPR_Dojkabacteria_WS6_RIFOXYB1_FULL_WS6_33_15","Bacteria_CPR_Dojkabacteria_WS6_BJP_IG2158_WS6_35_49","Bacteria_CPR_Dojkabacteria_WS6_GWC2_WS6_36_7","Bacteria_CPR_Dojkabacteria_WS6_GWF1_WS6_35_23_partial","Bacteria_CPR_Dojkabacteria_WS6_GWA2_WS6_37_6","Bacteria_Wirthbacteria_CG2_30_FULL_Wirthbacteria_54_11")
      }
      else {
      TOLoutgroup.labels<-c("Neurospora_crassa","Microsporum_canis","Uncinocarpus_reesii","Trichophyton_rubrum","Basipetospora_chlamydospora","Coccidioides_posadasii","Paracoccidioides_brasiliensis","Trichoderma_reesei","Coccidioides_immitis","Histoplasma_capsulatum","Talaromyces_occitanis","Talaromyces_marneffei")
      }
    })

  ## display proper citation based on associated manuscript
  output$TOLcitationText <- renderText({
      if (input$TOLphyloSelect == "Aspergillus and Penicillium, 81 taxa - Steenwyk et al. 2019") {
        paste("If you use this subtree, please cite: Steenwyk et al. 2019, mBio: 10.1128/mBio.00925-19")
      } else if (input$TOLphyloSelect == "Tree of life, 3,083 taxa - Hug et al. 2016") {
        paste("If you use this subtree, please cite: Hug et al. 2016, Nature Microbiology. doi: 10.1038/nmicrobiol.2016.48")
      } else 
        paste("If you use this subtree, please cite: Steenwyk et al. 2019, mBio: 10.1128/mBio.00925-19")
    })

  ## display table of taxa names
  TOLtipNames <- eventReactive(input$TOLgo, {
      a<-data.frame(TOLtree()$tip.label)
      # replace column name to "full list of taxa"
      colnames(a)[1]<-"full list of taxa for possible subtree"
      # return to df_subset
      return(a)
    })
  output$TOLtaxaTable <- renderTable(TOLtipNames())
  
  ## function to create plot
  output$TOLphyloPlot <- renderPlot({
    # root tree
    tree<-root(TOLtree(), outgroup = TOLoutgroup.labels(), resolve.root = TRUE) 
    # drop outgroup tips not in ingroup.labels
    ingroup.labels<-as.vector(TOLdata()$V1)
    outgroup.labels<-setdiff(TOLoutgroup.labels(),ingroup.labels)
    tree<-drop.tip(tree, outgroup.labels)
    # prune taxa not of interest
    pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
    if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
    # plot tree
    p<-try(plotTree(pruned.tree))
    if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
    p
    add.scale.bar(cex = 0.7, font = 2, col = "black")
  })
  
  ## save pdf
  output$TOLTreePlot<- downloadHandler(
    #Specify The File Name 
    filename = function() {
      paste("treehouse-",Sys.Date(),".pdf",sep= "")},
    content = function(file){
      # open the pdf
      pdf(file)
      # root tree
      tree<-root(TOLtree(), outgroup = TOLoutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(TOLdata()$V1)
      outgroup.labels<-setdiff(TOLoutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      add.scale.bar(cex = 0.7, font = 2, col = "black")
      dev.off()
    }
  )
  
  ## write treefile
  output$TOLNewick<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      # root tree
      tree<-root(TOLtree(), outgroup = TOLoutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(TOLdata()$V1)
      outgroup.labels<-setdiff(TOLoutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      # write tree file out
      write.tree(pruned.tree, file=file)
    }
  )

  ## write treefile
  output$TOLNewickNOBL<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      # root tree
      tree<-root(TOLtree(), outgroup = TOLoutgroup.labels(), resolve.root = TRUE)
      # drop outgroup tips not in ingroup.labels
      ingroup.labels<-as.vector(TOLdata()$V1)
      outgroup.labels<-setdiff(TOLoutgroup.labels(),ingroup.labels)
      tree<-drop.tip(tree, outgroup.labels)
      # prune taxa not of interest
      pruned.tree<-try(drop.tip(tree,tree$tip.label[-match(ingroup.labels, tree$tip.label)]), silent=TRUE)
      if("try-error" %in% class(pruned.tree)) stop("\nlist of tip names does not match names in phylogeny. Please check tip names again. A full list of tip names is available below\n\nR error:only 0's may be mixed with negative subscripts")
      # plot tree
      p<-try(plotTree(pruned.tree))
      if("try-error" %in% class(p)) p<-plot.phylo(pruned.tree)
      p
      # write tree file out
      pruned.tree$edge.length<-NULL
      write.tree(pruned.tree, file=file)
    }
  )

  ### USERTREE
  ## read in file reactively
  userData <- eventReactive(input$userGO, { 
    req(input$fileUser)
    inFile <- input$fileUser
    taxa.list<-read.table(inFile$datapath)
    return(taxa.list)
  })

  ## read in tree based on selected tree
  userTree <- eventReactive(input$userGO, {
    req(input$treeFile)
    inFile <- input$treeFile
    userTree <- read.tree(inFile$datapath)
  })

  ## display table of taxa names
  USERtipNames <- eventReactive(input$userGO, {
      a<-data.frame(userTree()$tip.label)
      # replace column name to "full list of taxa"
      colnames(a)[1]<-"full list of taxa for possible subtree"
      # return to df_subset
      return(a)
    })
  output$USERtaxaTable <- renderTable(USERtipNames())

  ## function to create plot
  output$userPhyloPlot <- renderPlot({
    # prune taxa not of interest
    ingroup.labels<-as.vector(userData()$V1)
    pruned.tree<-drop.tip(userTree(),userTree()$tip.label[-match(ingroup.labels, userTree()$tip.label)])
    # plot tree
    plotTree(pruned.tree)
    add.scale.bar(cex = 0.7, font = 2, col = "black")
  })
  
  ## save pdf
  output$userTreePlot<- downloadHandler(
    #Specify The File Name 
    filename = function() {
      paste("treehouse-",Sys.Date(),".pdf",sep= "")},
    content = function(file){
      # open the pdf
      pdf(file)
      # prune taxa not of interest
      ingroup.labels<-as.vector(userData()$V1)
      pruned.tree<-drop.tip(userTree(),userTree()$tip.label[-match(ingroup.labels, userTree()$tip.label)])
      # plot tree
      plotTree(pruned.tree)
      add.scale.bar(cex = 0.7, font = 2, col = "black")
      dev.off()
    }
  )

  ## write treefile
  output$userNewick<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      ingroup.labels<-as.vector(userData()$V1)
      pruned.tree<-drop.tip(userTree(),userTree()$tip.label[-match(ingroup.labels, userTree()$tip.label)])
      # write tree file out
      write.tree(pruned.tree, file=file)
    }
  )

  ## write treefile
  output$userNewickNOBL<- downloadHandler(
    # Specify the file name
    filename=function() {
      paste("treehouse-",Sys.Date(),".tre",sep= "")},
    content=function(file){
      ingroup.labels<-as.vector(userData()$V1)
      pruned.tree<-drop.tip(userTree(),userTree()$tip.label[-match(ingroup.labels, userTree()$tip.label)])
      pruned.tree$edge.length<-NULL
      # write tree file out
      write.tree(pruned.tree, file=file)
    }
  )

})