Loading SpliceWiz

For instructions on installing and configuring SpliceWiz, please see the Quick-Start vignette.

library(SpliceWiz)
#> Loading required package: NxtIRFdata
#> SpliceWiz package loaded with 2 threads
#> Use setSWthreads() to set the number of SpliceWiz threads


Reference Generation

First, define the path to the directory in which the reference should be stored. This directory will be made by SpliceWiz, but its parent directory must exist, otherwise an error will be returned.

ref_path <- "./Reference"


Create a SpliceWiz reference from user-defined FASTA and GTF files locally

Note that setting genome_path = "hg38" will prompt SpliceWiz to use the default files for nonPolyA and Mappability exclusion references in the generation of its reference. Valid options for genome_path are “hg38”, “hg19”, “mm10” and “mm9”.

buildRef(
    reference_path = ref_path,
    fasta = "genome.fa", gtf = "transcripts.gtf",
    genome_type = "hg38"
)


Prepare genome resources and building the reference as separate steps

buildRef() first runs getResources(), which prepares the genome and gene annotations by storing a compressed local copy in the resources subdirectory of the given reference path. Specifically, a binary compressed version of the FASTA file (a.k.a. TwoBitFile), and a gzipped GTF file. If fasta and/or gtf are https or ftp links, the resources will be downloaded from the internet (which may take a while).

After local compressed versions of the genome and gene annotations are prepared, buildRef() will proceed to generate the SpliceWiz reference.

Note that these two steps can be run separately. getResources() will prepare local compressed copies of the FASTA / GTF resources without generating the SpliceWiz reference. Running buildRef(), with reference_path specifying where the resources were prepared previously with getResources(), will perform the 2nd step (SpliceWiz reference generation) without needing to prepare the genome resources (in this case, set the parameters fasta = "" and gtf = "").

As an example, the below steps:

getResources(
    reference_path = ref_path,
    fasta = "genome.fa",
    gtf = "transcripts.gtf"
)

buildRef(
    reference_path = ref_path,
    fasta = "", gtf = "",
    genome_type = "hg38"
)

is equivalent to this:

buildRef(
    reference_path = ref_path,
    fasta = "genome.fa",
    gtf = "transcripts.gtf"
    genome_type = "hg38"
)


Overwriting an existing reference, but using the same annotations

To re-build and overwrite an existing reference, using the same resource annotations, set overwrite = TRUE

# Assuming hg38 genome:

buildRef(
    reference_path = ref_path,
    genome_type = "hg38",
    overwrite = TRUE
)


If buildRef() is run without setting overwrite = TRUE, it will terminate if the file SpliceWiz.ref.gz is found within the reference directory.


Create a SpliceWiz reference using web resources from Ensembl’s FTP

The following will first download the genome and gene annotation files from the online resource and store a local copy of it in a file cache, facilitated by BiocFileCache. Then, it uses the downloaded resource to create the SpliceWiz reference.

FTP <- "ftp://ftp.ensembl.org/pub/release-94/"

buildRef(
    reference_path = ref_path,
    fasta = paste0(FTP, "fasta/homo_sapiens/dna/",
        "Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz"), 
    gtf = paste0(FTP, "gtf/homo_sapiens/",
        "Homo_sapiens.GRCh38.94.chr.gtf.gz"),
    genome_type = "hg38"
)


Create a SpliceWiz reference using AnnotationHub resources

AnnotationHub contains Ensembl references for many genomes. To browse what is available:

require(AnnotationHub)
#> Loading required package: AnnotationHub
#> Loading required package: BiocGenerics
#> 
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
#>     union, unique, unsplit, which.max, which.min
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr

ah <- AnnotationHub()
query(ah, "Ensembl")
#> AnnotationHub with 36524 records
#> # snapshotDate(): 2024-04-29
#> # $dataprovider: Ensembl, FANTOM5,DLRP,IUPHAR,HPRD,STRING,SWISSPROT,TREMBL,E...
#> # $species: Mus musculus, Homo sapiens, Sus scrofa, Rattus norvegicus, Danio...
#> # $rdataclass: TwoBitFile, GRanges, EnsDb, SQLiteFile, data.frame, OrgDb, li...
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH5046"]]' 
#> 
#>              title               
#>   AH5046   | Ensembl Genes       
#>   AH5160   | Ensembl Genes       
#>   AH5311   | Ensembl Genes       
#>   AH5434   | Ensembl Genes       
#>   AH5435   | Ensembl EST Genes   
#>   ...        ...                 
#>   AH116714 | org.Mmu.eg.db.sqlite
#>   AH116715 | org.Ce.eg.db.sqlite 
#>   AH116716 | org.Xl.eg.db.sqlite 
#>   AH116717 | org.Sc.sgd.db.sqlite
#>   AH116718 | org.Dr.eg.db.sqlite

For a more specific query:

query(ah, c("Homo Sapiens", "release-94"))
#> AnnotationHub with 9 records
#> # snapshotDate(): 2024-04-29
#> # $dataprovider: Ensembl
#> # $species: Homo sapiens
#> # $rdataclass: TwoBitFile, GRanges
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["AH64628"]]' 
#> 
#>             title                                           
#>   AH64628 | Homo_sapiens.GRCh38.94.abinitio.gtf             
#>   AH64629 | Homo_sapiens.GRCh38.94.chr.gtf                  
#>   AH64630 | Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf 
#>   AH64631 | Homo_sapiens.GRCh38.94.gtf                      
#>   AH65744 | Homo_sapiens.GRCh38.cdna.all.2bit               
#>   AH65745 | Homo_sapiens.GRCh38.dna.primary_assembly.2bit   
#>   AH65746 | Homo_sapiens.GRCh38.dna_rm.primary_assembly.2bit
#>   AH65747 | Homo_sapiens.GRCh38.dna_sm.primary_assembly.2bit
#>   AH65748 | Homo_sapiens.GRCh38.ncrna.2bit

We wish to fetch “AH65745” and “AH64631” which contains the desired FASTA and GTF files, respectively. To build a reference using these resources:

buildRef(
    reference_path = ref_path,
    fasta = "AH65745",
    gtf = "AH64631",
    genome_type = "hg38"
)

Build-Reference-methods will recognise the inputs of fasta and gtf as AnnotationHub resources if they begin with “AH”.

Create a SpliceWiz reference from species other than human or mouse

For human and mouse genomes, we highly recommend specifying genome_type as the default mappability file is used to exclude intronic regions with repeat sequences from intron retention analysis. For other species, one could generate a SpliceWiz reference without this reference:

buildRef(
    reference_path = ref_path,
    fasta = "genome.fa", gtf = "transcripts.gtf",
    genome_type = ""
)


If one wishes to prepare a Mappability Exclusion for species other than human or mouse, please see the Calculating Mappability Exclusions using STAR section below.

(NEW) Gene ontology annotations

For human and mouse genomes, gene ontology annotations are automatically generated. This is inferred by specifying genome_type to the human or mouse genome. For other species, or to specify human/mouse, this should be specified in the ontologySpecies parameter of buildRef().

Only Ensembl/orgDB resources are supported (for now). For a list of available species:

getAvailableGO()
#>    [1] "Triticum aestivum"                                         
#>    [2] "Triticum aestivum_subsp._aestivum"                         
#>    [3] "Triticum vulgare"                                          
#>    [4] "Brassica napus"                                            
#>    [5] "Arachis hypogaea"                                          
#>    [6] "Hibiscus syriacus"                                         
#>    [7] "Acridium cancellatum"                                      
#>    [8] "Schistocerca cancellata"                                   
#>    [9] "Triticum dicoccoides"                                      
#>   [10] "Triticum turgidum_subsp._dicoccoides"                      
#>   [11] "Triticum turgidum_var._dicoccoides"                        
#>   [12] "Dendrohyas sarda"                                          
#>   [13] "Hyla arborea_sarda"                                        
#>   [14] "Hyla sarda"                                                
#>   [15] "Locusta gregaria"                                          
#>   [16] "Schistocerca gregaria"                                     
#>   [17] "Gossypium hirsutum"                                        
#>   [18] "Gossypium hirsutum_subsp._mexicanum"                       
#>   [19] "Gossypium lanceolatum"                                     
#>   [20] "Gossypium purpurascens"                                    
#>   [21] "Camelina sativa"                                           
#>   [22] "Carassius auratus_gibelio"                                 
#>   [23] "Carassius gibelio_gibelio"                                 
#>   [24] "Carassius gibelio"                                         
#>   [25] "Carassius gibelio_subsp._gibelio"                          
#>   [26] "Cyprinus gibelio"                                          
#>   [27] "Schistocerca piceifrons"                                   
#>   [28] "Papaver somniferum"                                        
#>   [29] "Zingiber officinale"                                       
#>   [30] "Trichomonas vaginalis_G3"                                  
#>   [31] "Trichomonas vaginalis_strain_G3"                           
#>   [32] "Carassius auratus"                                         
#>   [33] "Carassius carassius_auratus"                               
#>   [34] "Cyprinus auratus"                                          
#>   [35] "Helianthus annuus"                                         
#>   [36] "Schistocerca americana"                                    
#>   [37] "Acipenser ruthenus"                                        
#>   [38] "Schistocerca serialis_cubense"                             
#>   [39] "Panicum virgatum"                                          
#>   [40] "Nicotiana tabacum"                                         
#>   [41] "Oncorhynchus mykiss"                                       
#>   [42] "Oncorhynchus nerka_mykiss"                                 
#>   [43] "Parasalmo mykiss"                                          
#>   [44] "Salmo mykiss"                                              
#>   [45] "Schistocerca nitens"                                       
#>   [46] "Schistocerca vaga"                                         
#>   [47] "Salvia splendens"                                          
#>   [48] "Carassius carassius"                                       
#>   [49] "Cyprinus carassius"                                        
#>   [50] "Vicia villosa"                                             
#>   [51] "Camellia sinensis"                                         
#>   [52] "Thea sinensis"                                             
#>   [53] "Oncorhynchus keta"                                         
#>   [54] "Salmo keta"                                                
#>   [55] "Pisum sativum"                                             
#>   [56] "Salmo salar"                                               
#>   [57] "Raphanus sativus"                                          
#>   [58] "Oncorhynchus kisutch"                                      
#>   [59] "Oncorhyncus kisutch"                                       
#>   [60] "Salmo kisatch"                                             
#>   [61] "Lolium rigidum"                                            
#>   [62] "Aegilops squarrosa_subsp._squarrosa"                       
#>   [63] "Aegilops squarrosa"                                        
#>   [64] "Aegilops tauschii"                                         
#>   [65] "Patropyrum tauschii_subsp._tauschii"                       
#>   [66] "Patropyrum tauschii"                                       
#>   [67] "Triticum aegilops"                                         
#>   [68] "Triticum tauschii"                                         
#>   [69] "Salmo trutta"                                              
#>   [70] "Cryptomeria japonica"                                      
#>   [71] "Coregonus clupeaformis"                                    
#>   [72] "Salmo clupeaformis"                                        
#>   [73] "Oncorhynchus gorbuscha"                                    
#>   [74] "Salmo gorbuscha"                                           
#>   [75] "Cyprinus carpio"                                           
#>   [76] "Glycine max_subsp._soja"                                   
#>   [77] "Glycine soja"                                              
#>   [78] "Salmo fontinalis"                                          
#>   [79] "Salvelinus fontinalis"                                     
#>   [80] "Glycine max"                                               
#>   [81] "Phaseolus max"                                             
#>   [82] "Chenopodium quinoa"                                        
#>   [83] "Hordeum sativum"                                           
#>   [84] "Hordeum vulgare_subsp._vulgare"                            
#>   [85] "Hordeum vulgare_var._nudum"                                
#>   [86] "Hordeum vulgare_var._vulgare"                              
#>   [87] "Festuca perennis_(L.)_Columbus_&_J.P.Sm.,_2010"            
#>   [88] "Festuca perennis"                                          
#>   [89] "Lolium perenne"                                            
#>   [90] "Lolium vulgare"                                            
#>   [91] "Coffea arabica"                                            
#>   [92] "Barbus grahami"                                            
#>   [93] "Sinocyclocheilus grahami"                                  
#>   [94] "Sinocyclocheilus rhinocerous"                              
#>   [95] "Gossypium arboreum"                                        
#>   [96] "Brassica oleracea"                                         
#>   [97] "Malus sylvestris"                                          
#>   [98] "Pyrus malus_var._sylvestris"                               
#>   [99] "Astyanax mexicanus"                                        
#>  [100] "Tetragonopterus mexicanus"                                 
#>  [101] "Arachis stenosperma"                                       
#>  [102] "Prosopis alba"                                             
#>  [103] "Sinocyclocheilus anshuiensis"                              
#>  [104] "Brassica rapa"                                             
#>  [105] "Lactuca sativa"                                            
#>  [106] "Dreissena polymorpha"                                      
#>  [107] "Mytilus polymorphus"                                       
#>  [108] "Hydractinia symbiolongicarpus"                             
#>  [109] "Hevea brasiliensis"                                        
#>  [110] "Oncorhynchus tschawytscha"                                 
#>  [111] "Oncorhynchus tshawytscha"                                  
#>  [112] "Salmo tshawytscha"                                         
#>  [113] "Arachis ipaensis"                                          
#>  [114] "Zea mays"                                                  
#>  [115] "Zea mays_var._japonica"                                    
#>  [116] "Salmo namaycush"                                           
#>  [117] "Salvelinus namaycush"                                      
#>  [118] "Capsicum annuum"                                           
#>  [119] "Brienomyrus brachyistius"                                  
#>  [120] "Marcusenius brachyistius"                                  
#>  [121] "Convolvulus nil"                                           
#>  [122] "Ipomoea nil"                                               
#>  [123] "Pharbitis nil"                                             
#>  [124] "Olea europaea_subsp._europaea_var._sylvestris"             
#>  [125] "Olea europaea_var._oleaster"                               
#>  [126] "Olea europaea_var._sylvestris"                             
#>  [127] "Olea europea_subsp._sylvestris"                            
#>  [128] "Alosa sapidissima"                                         
#>  [129] "Clupea sapidissima"                                        
#>  [130] "Carpiodes asiaticus"                                       
#>  [131] "Myxocyprinus asiaticus"                                    
#>  [132] "Actinidia eriantha"                                        
#>  [133] "Gossypium raimondii"                                       
#>  [134] "Salmo alpinus"                                             
#>  [135] "Salvelinus alpinus"                                        
#>  [136] "Catostomus texanus"                                        
#>  [137] "Xyrauchen texanus"                                         
#>  [138] "Doryrhamphus excisus"                                      
#>  [139] "Quercus lobata"                                            
#>  [140] "Malus communis"                                            
#>  [141] "Malus domestica"                                           
#>  [142] "Malus pumila_auct."                                        
#>  [143] "Malus pumila_var._domestica"                               
#>  [144] "Malus sylvestris_var._domestica"                           
#>  [145] "Malus x_domestica"                                         
#>  [146] "Pyrus malus"                                               
#>  [147] "Pyrus malus_var._domestica"                                
#>  [148] "Quercus suber"                                             
#>  [149] "Oncorhynchus nerka"                                        
#>  [150] "Salmo nerka"                                               
#>  [151] "Nicotiana tomentosiformis"                                 
#>  [152] "Carya illinoensis"                                         
#>  [153] "Carya illinoinensis"                                       
#>  [154] "Mercenaria mercenaria"                                     
#>  [155] "Venus mercenaria"                                          
#>  [156] "Quercus robur"                                             
#>  [157] "Durio zibethinus"                                          
#>  [158] "Pongo abelii"                                              
#>  [159] "Pongo pygmaeus_abelii"                                     
#>  [160] "Pongo pygmaeus_abeli"                                      
#>  [161] "Mya arenaria"                                              
#>  [162] "Arachis duranensis"                                        
#>  [163] "Arachis spegazzinii"                                       
#>  [164] "Pyrus x_bretschneideri"                                    
#>  [165] "Trifolium pratense"                                        
#>  [166] "Gorilla gorilla_gorilla"                                   
#>  [167] "Cobitis anguillicaudata"                                   
#>  [168] "Misgurnus anguillicaudatus"                                
#>  [169] "Scaphiopus bombifrons"                                     
#>  [170] "Spea bombifrons"                                           
#>  [171] "Haliotis rufenscens"                                       
#>  [172] "Haliotis rufescens"                                        
#>  [173] "Oreochromis nilotica"                                      
#>  [174] "Oreochromis niloticus"                                     
#>  [175] "Perca nilotica"                                            
#>  [176] "Tilapia nilotica"                                          
#>  [177] "Acropora convexa"                                          
#>  [178] "Acropora millepora"                                        
#>  [179] "Acropora singularis"                                       
#>  [180] "Cebus apella"                                              
#>  [181] "Sapajus apella"                                            
#>  [182] "Simia apella"                                              
#>  [183] "Eucalyptus grandis"                                        
#>  [184] "Dasypus novemcinctus"                                      
#>  [185] "Callithrix jacchus_jacchus"                                
#>  [186] "Callithrix jacchus"                                        
#>  [187] "Simia jacchus"                                             
#>  [188] "Pistacia vera"                                             
#>  [189] "greater Indian_fruit_bat"                                  
#>  [190] "Pteropus giganteus"                                        
#>  [191] "Pteropus medius"                                           
#>  [192] "Salvia miltiorhiza"                                        
#>  [193] "Salvia miltiorrhiza"                                       
#>  [194] "Daphnia pulicaria"                                         
#>  [195] "Magnolia sinica"                                           
#>  [196] "Manglietia sinica"                                         
#>  [197] "Manglietiastrum sinicum"                                   
#>  [198] "Pachylarnax sinica_(Y.W.Law)_N.H.Xia_&_C.Y.Wu"             
#>  [199] "Rosa chinensis"                                            
#>  [200] "Rosa indica_auct.,_non_L."                                 
#>  [201] "Mytilus californianus"                                     
#>  [202] "Pteropus vampyrus"                                         
#>  [203] "Vespertilio vampyrus"                                      
#>  [204] "Chinemys reevesii"                                         
#>  [205] "Chinemys reevesi"                                          
#>  [206] "Emys reevesii"                                             
#>  [207] "Geoclemys reevesii"                                        
#>  [208] "Geoclemys reevessi"                                        
#>  [209] "Mauremys reevesii"                                         
#>  [210] "Mauremys reevesi"                                          
#>  [211] "Choloepus brasiliensis_Fitzinger_1871"                     
#>  [212] "Choloepus brasiliensis"                                    
#>  [213] "Choloepus didactylus"                                      
#>  [214] "Macaca nemestrina"                                         
#>  [215] "Simia nemestrina"                                          
#>  [216] "Bubalus arnee_carabanensis"                                
#>  [217] "Bubalus bubalis_carabanesis"                               
#>  [218] "Bubalus carabanensis_carabanensis"                         
#>  [219] "Bubalus carabanensis"                                      
#>  [220] "Lotus corniculatus_var._japonicus"                         
#>  [221] "Lotus japonicus"                                           
#>  [222] "Nicotiana sylvestris"                                      
#>  [223] "Tupaia belangeri_chinensis"                                
#>  [224] "Tupaia chinensis"                                          
#>  [225] "Clarias gariepinus"                                        
#>  [226] "Clarias lazera"                                            
#>  [227] "Silurus gariepinus"                                        
#>  [228] "Canis dingo"                                               
#>  [229] "Canis familiaris_dingo"                                    
#>  [230] "Canis lupus_dingo"                                         
#>  [231] "Barbus tetrazona"                                          
#>  [232] "Capoeta tetrazona"                                         
#>  [233] "Puntigrus tetrazona"                                       
#>  [234] "Puntius tetrazona"                                         
#>  [235] "Systomus tetrazona"                                        
#>  [236] "Lycium ferocissimum"                                       
#>  [237] "Nicotiana attenuata"                                       
#>  [238] "Denticeps clupeoides"                                      
#>  [239] "Octodon degus"                                             
#>  [240] "Haliotis rubra"                                            
#>  [241] "Aedes albopictus"                                          
#>  [242] "Stegomyia albopicta"                                       
#>  [243] "Spinacia oleracea"                                         
#>  [244] "Paramecium aurelia_syngen_4"                               
#>  [245] "Paramecium tetraurelia"                                    
#>  [246] "Salvia hispanica"                                          
#>  [247] "Medicago truncatula"                                       
#>  [248] "Crassostrea virginica"                                     
#>  [249] "Ostrea virginica"                                          
#>  [250] "Felis catus"                                               
#>  [251] "Felis domesticus"                                          
#>  [252] "Felis silvestris_catus"                                    
#>  [253] "Anubis baboon"                                             
#>  [254] "Papio anubis"                                              
#>  [255] "Papio cynocephalus_anubis"                                 
#>  [256] "Papio doguera"                                             
#>  [257] "Papio hamadryas_anubis"                                    
#>  [258] "Papio hamadryas_doguera"                                   
#>  [259] "Pongo pygmaeus"                                            
#>  [260] "Simia pygmaeus"                                            
#>  [261] "Sorex etruscus"                                            
#>  [262] "Suncus etruscus"                                           
#>  [263] "Prosopis cineraria"                                        
#>  [264] "Nycticebus coucang"                                        
#>  [265] "Tardigradus coucang"                                       
#>  [266] "Rhododendron vialii"                                       
#>  [267] "Pan paniscus"                                              
#>  [268] "Nematostella vectensis"                                    
#>  [269] "Ixodes dammini"                                            
#>  [270] "Ixodes scapularis"                                         
#>  [271] "Lupinus angustifolius"                                     
#>  [272] "Ipomoea triloba"                                           
#>  [273] "Equus asinus"                                              
#>  [274] "Emiliania huxleyi_CCMP1516"                                
#>  [275] "Emiliania huxleyi_CCMP2090"                                
#>  [276] "Mangifera indica"                                          
#>  [277] "Pteropus alecto"                                           
#>  [278] "Rana temporaria"                                           
#>  [279] "Crassostrea gigas"                                         
#>  [280] "Ostrea gigas"                                              
#>  [281] "Crassostrea angulata"                                      
#>  [282] "Etheostoma spectabile"                                     
#>  [283] "Poecilichthys spectabilis"                                 
#>  [284] "Macadamia integrifolia"                                    
#>  [285] "Megalobrama amblycephala"                                  
#>  [286] "Halichoerus grypus"                                        
#>  [287] "Phoca grypus"                                              
#>  [288] "Juglans regia"                                             
#>  [289] "Selaginella moellendorffii"                                
#>  [290] "Selaginella moellendorfii"                                 
#>  [291] "Pleuronectes platessa"                                     
#>  [292] "Presbytis francoisi"                                       
#>  [293] "Trachypithecus francoisi"                                  
#>  [294] "Tripterygium wilfordii"                                    
#>  [295] "Argiope bruennichi"                                        
#>  [296] "Lepus cuniculus"                                           
#>  [297] "Oryctolagus cuniculus"                                     
#>  [298] "Huro salmoides"                                            
#>  [299] "Labrus salmoides"                                          
#>  [300] "Labrus salmonides"                                         
#>  [301] "Micropterus nigricans"                                     
#>  [302] "Micropterus salmoides"                                     
#>  [303] "Solanum stenotomum"                                        
#>  [304] "Heterocephalus glaber"                                     
#>  [305] "Neosciurus carolinensis"                                   
#>  [306] "Sciurus carolinensis"                                      
#>  [307] "Cervus elaphus"                                            
#>  [308] "Polyodon spathula"                                         
#>  [309] "Squalus spathula"                                          
#>  [310] "Gadus chalcogrammus"                                       
#>  [311] "Theragra chalcogramma_finnmarchica"                        
#>  [312] "Theragra chalcogramma"                                     
#>  [313] "Theragra finnmarchica"                                     
#>  [314] "Nothobranchius furzeri"                                    
#>  [315] "Bos bubalis"                                               
#>  [316] "Bubalus arnee_bubalis"                                     
#>  [317] "Bubalus bubalis"                                           
#>  [318] "Pleuronectes solea"                                        
#>  [319] "Solea solea"                                               
#>  [320] "Solea vulgaris"                                            
#>  [321] "Mastomys coucha"                                           
#>  [322] "Praomys coucha"                                            
#>  [323] "Impatiens glandulifera"                                    
#>  [324] "Dermacentor andersoni"                                     
#>  [325] "Felis nebulosa"                                            
#>  [326] "Neofelis nebulosa"                                         
#>  [327] "Pteropus egyptiacus"                                       
#>  [328] "Rousettus aegyptiacus"                                     
#>  [329] "Rousettus aegypticus"                                      
#>  [330] "Rousettus egyptiacus"                                      
#>  [331] "Phoenix dactylifera"                                       
#>  [332] "Pimephales promelas"                                       
#>  [333] "Ostrea edulis"                                             
#>  [334] "Cebus capucinus_imitator"                                  
#>  [335] "Cebus imitator"                                            
#>  [336] "Peromyscus maniculatus_bairdii"                            
#>  [337] "Gasterosteus pungitius"                                    
#>  [338] "Pungitius pungitius"                                       
#>  [339] "Populus alba"                                              
#>  [340] "Cricetus auratus"                                          
#>  [341] "Golden hamsters"                                           
#>  [342] "Mesocricetus auratus"                                      
#>  [343] "Syrian hamsters"                                           
#>  [344] "Chromis aureus"                                            
#>  [345] "Oreochromis aurea"                                         
#>  [346] "Oreochromis aureus"                                        
#>  [347] "Daucus carota_subsp._sativus"                              
#>  [348] "Daucus carota_var._sativus"                                
#>  [349] "Dermacentor silvarum"                                      
#>  [350] "Hylobates syndactylus"                                     
#>  [351] "Simia syndactyla"                                          
#>  [352] "Symphalangus syndactylus"                                  
#>  [353] "Saccharolobus solfataricus"                                
#>  [354] "Sulfolobus solfataricus"                                   
#>  [355] "Felis geoffroyi"                                           
#>  [356] "Leopardus geoffroyi"                                       
#>  [357] "Oncifelis geoffroyi"                                       
#>  [358] "Felis yagouaroundi"                                        
#>  [359] "Herpailurus yagouaroundi"                                  
#>  [360] "Herpailurus yaguarondi"                                    
#>  [361] "Puma yagouaroundii"                                        
#>  [362] "Puma yagouaroundi"                                         
#>  [363] "Cervus canadensis"                                         
#>  [364] "Populus diversifolia"                                      
#>  [365] "Populus euphratica"                                        
#>  [366] "Cucurbita pepo_subsp._pepo"                                
#>  [367] "Cucurbita pepo_var._medullosa"                             
#>  [368] "Cucurbita pepo_var._pepo"                                  
#>  [369] "Macaca cynomolgus"                                         
#>  [370] "Macaca fascicularis"                                       
#>  [371] "Macaca irus"                                               
#>  [372] "Simia fascicularis"                                        
#>  [373] "Emys muticus"                                              
#>  [374] "Geoclemmys mutica"                                         
#>  [375] "Mauremys mutica"                                           
#>  [376] "Suricata suricatta"                                        
#>  [377] "Viverra suricatta"                                         
#>  [378] "Hylobates moloch"                                          
#>  [379] "Simia moloch"                                              
#>  [380] "Solanum dulcamara"                                         
#>  [381] "Cucurbita moschata"                                        
#>  [382] "Coffea eugeniodes"                                         
#>  [383] "Coffea eugenioides"                                        
#>  [384] "Cucurbita maxima"                                          
#>  [385] "Colobus tephrosceles"                                      
#>  [386] "Piliocolobus tephrosceles"                                 
#>  [387] "Procolobus badius_tephrosceles"                            
#>  [388] "Procolobus rufomitratus_tephrosceles"                      
#>  [389] "Labrus bergylta"                                           
#>  [390] "Centropristis striata"                                     
#>  [391] "Labrus striatus"                                           
#>  [392] "Oryza sativa_(japonica_cultivar-group)"                    
#>  [393] "Oryza sativa_Japonica_Group"                               
#>  [394] "Oryza sativa_subsp._japonica"                              
#>  [395] "Jaculus jaculus"                                           
#>  [396] "Mus jaculus"                                               
#>  [397] "Dioscorea cayenensis_subsp._rotundata"                     
#>  [398] "Dioscorea rotundata"                                       
#>  [399] "Cercopithecus aethiops_sabaeus"                            
#>  [400] "Cercopithecus sabaeus"                                     
#>  [401] "Cercopithecus sabeus"                                      
#>  [402] "Chlorocebus aethiops_sabaeus"                              
#>  [403] "Chlorocebus aethiops_sabeus"                               
#>  [404] "Chlorocebus sabaeus"                                       
#>  [405] "Chlorocebus sabeus"                                        
#>  [406] "Simia sabaea"                                              
#>  [407] "Marmota monax"                                             
#>  [408] "Mus monax"                                                 
#>  [409] "Pygathrix roxellana"                                       
#>  [410] "Rhinopithecus roxellana"                                   
#>  [411] "Semnopithecus roxellana"                                   
#>  [412] "Callorhinus ursinus"                                       
#>  [413] "Callorhynus ursius"                                        
#>  [414] "Phoca ursina"                                              
#>  [415] "Cricetulus barabensis_griseus"                             
#>  [416] "Cricetulus griseus"                                        
#>  [417] "Elephantulus edwardii"                                     
#>  [418] "Macroscelides edwardii"                                    
#>  [419] "Cobitis heteroclita"                                       
#>  [420] "Fundulus heteroclitus"                                     
#>  [421] "Neothunnus macropterus"                                    
#>  [422] "Scomber albacares"                                         
#>  [423] "Thunnus albacares"                                         
#>  [424] "Telopea speciosissima"                                     
#>  [425] "Danio aesculapii"                                          
#>  [426] "Marmota marmota_marmota"                                   
#>  [427] "Apodemus sylvaticus"                                       
#>  [428] "Mus sylvaticus"                                            
#>  [429] "Sylvaemus sylvaticus"                                      
#>  [430] "Populus balsamifera_subsp._trichocarpa"                    
#>  [431] "Populus trichocarpa"                                       
#>  [432] "Mercurialis annua"                                         
#>  [433] "Syzygium oleosum"                                          
#>  [434] "Citellus tridecemlineatus"                                 
#>  [435] "Ictidomys tridecemlineatus"                                
#>  [436] "Spermophilus tridecemlineatus"                             
#>  [437] "Ovis ammon_aries"                                          
#>  [438] "Ovis aries"                                                
#>  [439] "Ovis orientalis_aries"                                     
#>  [440] "Ovis ovis"                                                 
#>  [441] "Solanum verrucosum"                                        
#>  [442] "Leo pardus"                                                
#>  [443] "Panthera pardus"                                           
#>  [444] "Microtus oregoni"                                          
#>  [445] "Arabidopsis lyrata_subsp._lyrata"                          
#>  [446] "Arabis lyrata_subsp._lyrata"                               
#>  [447] "Arabis lyrata"                                             
#>  [448] "Cardaminopsis lyrata"                                      
#>  [449] "Manihot esculenta"                                         
#>  [450] "Manihot utilissima"                                        
#>  [451] "Mustela erminea"                                           
#>  [452] "Phaseolus unguiculatus"                                    
#>  [453] "Vigna unguiculata"                                         
#>  [454] "Lycopersicon pennellii_(Correll)_D'Arcy,_1982"             
#>  [455] "Solanum pennellii_Correll,_1958"                           
#>  [456] "Solanum pennellii"                                         
#>  [457] "Setaria viridis"                                           
#>  [458] "Musa AA_Group"                                             
#>  [459] "Musa acuminata_AA_Group"                                   
#>  [460] "Musa acuminata"                                            
#>  [461] "Musa nana"                                                 
#>  [462] "Gymnostomus macrolepis"                                    
#>  [463] "Onychostoma macrolepis"                                    
#>  [464] "Scaphesthes macrolepis"                                    
#>  [465] "Varicorhinus macrolepis"                                   
#>  [466] "Varicorhinus (Scaphesthes)_macrolepis"                     
#>  [467] "Oryza glaberrima"                                          
#>  [468] "Pelteobagrus fulvidraco"                                   
#>  [469] "Pimelodus fulvidraco"                                      
#>  [470] "Pseudobagrus fulvidraco"                                   
#>  [471] "Tachysurus fulvidraco"                                     
#>  [472] "Hylobates concolor_leucogenys"                             
#>  [473] "Hylobates concolor_leucogyneus"                            
#>  [474] "Hylobates leucogenys_leucogenys"                           
#>  [475] "Hylobates leucogenys"                                      
#>  [476] "Nomascus leucogenys_leucogenys"                            
#>  [477] "Nomascus leucogenys"                                       
#>  [478] "Nomascus leukogenys"                                       
#>  [479] "Nannospalax ehrenbergi_galili"                             
#>  [480] "Nannospalax galili"                                        
#>  [481] "Spalax galili"                                             
#>  [482] "Equus caballus"                                            
#>  [483] "Equus przewalskii_f._caballus"                             
#>  [484] "Equus przewalskii_forma_caballus"                          
#>  [485] "Thunnus maccoyii"                                          
#>  [486] "Thynnus maccoyii"                                          
#>  [487] "Chromis diagramma"                                         
#>  [488] "Simochromis diagramma"                                     
#>  [489] "Diplophysa dalaica"                                        
#>  [490] "Triplophysa dalaica"                                       
#>  [491] "Panthera tigris"                                           
#>  [492] "Strongylocentrotus purpuratus"                             
#>  [493] "Lucioperca lucioperca"                                     
#>  [494] "Perca lucioperca"                                          
#>  [495] "Sander lucioperca"                                         
#>  [496] "Stizostedion lucioperca"                                   
#>  [497] "Dipodomys spectabilis"                                     
#>  [498] "Acinonyx jubatus"                                          
#>  [499] "Felis jubata"                                              
#>  [500] "Conyza canadensis"                                         
#>  [501] "Erigeron canadensis"                                       
#>  [502] "Mustela lutreola"                                          
#>  [503] "Camelus bactrianus_ferus"                                  
#>  [504] "Camelus ferus"                                             
#>  [505] "Cajanus cajan"                                             
#>  [506] "Didelphys domestica"                                       
#>  [507] "Monodelphis domestica"                                     
#>  [508] "Pygathrix bieti"                                           
#>  [509] "Rhinopithecus bieti"                                       
#>  [510] "Saimiri boliviensis"                                       
#>  [511] "Hesperomys eremicus"                                       
#>  [512] "Peromyscus eremicus"                                       
#>  [513] "Arabidopsis salsuginea"                                    
#>  [514] "Eutrema salsugineum"                                       
#>  [515] "Hesperis salsuginea"                                       
#>  [516] "Sisymbrium salsugineum"                                    
#>  [517] "Stenophragma salsugineum"                                  
#>  [518] "Thellungiella salsuginea"                                  
#>  [519] "Thelypodium salsugineum"                                   
#>  [520] "Coetomys damarensis"                                       
#>  [521] "Cryptomys damarensis"                                      
#>  [522] "Fukomys damarensis"                                        
#>  [523] "Gadus morhua"                                              
#>  [524] "Leptonychotes weddellii"                                   
#>  [525] "Leptonychotes weddelli"                                    
#>  [526] "Otaria weddellii"                                          
#>  [527] "Grammomys dolichurus_surdaster"                            
#>  [528] "Grammomys surdaster"                                       
#>  [529] "Thamnomys surdaster"                                       
#>  [530] "Solanum tuberosum"                                         
#>  [531] "Andropogon sorghum"                                        
#>  [532] "Sorghum bicolor"                                           
#>  [533] "Sorghum bicolor_subsp._bicolor"                            
#>  [534] "Sorghum nervosum"                                          
#>  [535] "Sorghum saccharatum"                                       
#>  [536] "Sorghum vulgare"                                           
#>  [537] "Holocentrus calcarifer"                                    
#>  [538] "Lates calcarifer"                                          
#>  [539] "Hippopotamus amphibius_kiboko"                             
#>  [540] "Ixodes sanguineus"                                         
#>  [541] "Rhipicephalus sanguineus"                                  
#>  [542] "Clupea harengus_harengus"                                  
#>  [543] "Clupea harengus"                                           
#>  [544] "Bos indicus_x_Bos_taurus"                                  
#>  [545] "Bos primigenius_indicus_x_Bos_primigenius_taurus"          
#>  [546] "Bos taurus_indicus_x_Bos_taurus_taurus"                    
#>  [547] "Bos taurus_x_Bos_indicus"                                  
#>  [548] "Chrysochloris asiatica"                                    
#>  [549] "Talpa asiatica"                                            
#>  [550] "Macacus gelada"                                            
#>  [551] "Theropithecus gelada"                                      
#>  [552] "Bufo bufo"                                                 
#>  [553] "Rana bufo"                                                 
#>  [554] "Maylandia zebra"                                           
#>  [555] "Metriaclima zebra"                                         
#>  [556] "Pseudotropheus sp._'Pseudotropheus_zebra_complex'"         
#>  [557] "Pseudotropheus zebra"                                      
#>  [558] "Otaria californiana"                                       
#>  [559] "Zalophus californianus"                                    
#>  [560] "Ictalurus punctatus"                                       
#>  [561] "Silurus punctatus"                                         
#>  [562] "Mus caroli"                                                
#>  [563] "Mus formosanus"                                            
#>  [564] "Oryx dammah"                                               
#>  [565] "Camelus dromedarius"                                       
#>  [566] "Asparagus officinalis"                                     
#>  [567] "Amaranthus gangeticus"                                     
#>  [568] "Amaranthus mangostanus"                                    
#>  [569] "Amaranthus tricolor"                                       
#>  [570] "Pneumatophorus japonicus"                                  
#>  [571] "Scomber japonicus"                                         
#>  [572] "Lutra lutra"                                               
#>  [573] "Peromyscus leucopus"                                       
#>  [574] "Perca fluviatilis"                                         
#>  [575] "Pagothenia bernacchii"                                     
#>  [576] "Pseudotrematomus bernacchii"                               
#>  [577] "Trematomus bernacchii"                                     
#>  [578] "Trematomus bernacchi"                                      
#>  [579] "Phascolarctos cinereus"                                    
#>  [580] "Mustela furo"                                              
#>  [581] "Mustela putorius_furo"                                     
#>  [582] "Chaetochloa italica"                                       
#>  [583] "Panicum italicum"                                          
#>  [584] "Pennisetum macrochaetum"                                   
#>  [585] "Setaria italica"                                           
#>  [586] "Setaria viridis_subsp._italica"                            
#>  [587] "Elaeis guineensis"                                         
#>  [588] "Mus rattus"                                                
#>  [589] "Rattus rattoides"                                          
#>  [590] "Rattus rattus"                                             
#>  [591] "Rattus wroughtoni"                                         
#>  [592] "Acropora digitifera"                                       
#>  [593] "Madrepora digitifera"                                      
#>  [594] "Leo leo"                                                   
#>  [595] "Panthera leo"                                              
#>  [596] "Echinops telfairii"                                        
#>  [597] "Echinops telfairi"                                         
#>  [598] "Madrepora verrucosa"                                       
#>  [599] "Pocillopora danae"                                         
#>  [600] "Pocillopora verrucosa"                                     
#>  [601] "Myotis daubentonii"                                        
#>  [602] "Myotis daubentoni"                                         
#>  [603] "Vespertilio daubentonii"                                   
#>  [604] "Limia formosa"                                             
#>  [605] "Mollienesia formosa"                                       
#>  [606] "Poecilia formosa"                                          
#>  [607] "Phyllostomus discolor"                                     
#>  [608] "Aurata aurata"                                             
#>  [609] "Sparus aurata"                                             
#>  [610] "Sparus auratus"                                            
#>  [611] "Microcebus murinus"                                        
#>  [612] "Peromyscus californicus_insignis"                          
#>  [613] "Peromyscus californicus_subsp._insignis"                   
#>  [614] "Galago garnettii"                                          
#>  [615] "Galago garnetti"                                           
#>  [616] "Otolemur garnettii"                                        
#>  [617] "Arvicanthis niloticus"                                     
#>  [618] "Didelphis ursina"                                          
#>  [619] "Vombatus ursinus"                                          
#>  [620] "Phaseolus angularis"                                       
#>  [621] "Vigna angularis"                                           
#>  [622] "Haitia acuta"                                              
#>  [623] "Physa acuta"                                               
#>  [624] "Physa heterostropha"                                       
#>  [625] "Physa integra"                                             
#>  [626] "Physella acuta"                                            
#>  [627] "Physella heterostropha"                                    
#>  [628] "Physella integra"                                          
#>  [629] "Ctenopharyngodon idella"                                   
#>  [630] "Ctenopharyngodon idellus"                                  
#>  [631] "Leuciscus idella"                                          
#>  [632] "Thalassophryne amazonica"                                  
#>  [633] "Cyprinus rohita"                                           
#>  [634] "Labeo rohita"                                              
#>  [635] "Talpa occidentalis"                                        
#>  [636] "Bombina bombina"                                           
#>  [637] "Rana bombina"                                              
#>  [638] "Cavia aperea_porcellus"                                    
#>  [639] "Cavia cobaya"                                              
#>  [640] "Cavia porcellus"                                           
#>  [641] "Mus porcellus"                                             
#>  [642] "Odocoileus virginianus"                                    
#>  [643] "Amphibalanus amphitrite"                                   
#>  [644] "Balanus amphitrite"                                        
#>  [645] "Panicum hallii"                                            
#>  [646] "Angill angill"                                             
#>  [647] "Anguilla anguilla_anguilla"                                
#>  [648] "Anguilla anguilla"                                         
#>  [649] "Muraena anguilla"                                          
#>  [650] "Orcinus orca"                                              
#>  [651] "Cannabis sativa"                                           
#>  [652] "Penaeus bubulus"                                           
#>  [653] "Penaeus carinatus"                                         
#>  [654] "Penaeus durbani"                                           
#>  [655] "Penaeus monodon"                                           
#>  [656] "Penaeus (Penaeus)_monodon"                                 
#>  [657] "Didelphis vulpecula"                                       
#>  [658] "Trichosurus vulpecula"                                     
#>  [659] "Myotis lucifugus"                                          
#>  [660] "Vespertilio lucifugus"                                     
#>  [661] "Brachypodium distachyon"                                   
#>  [662] "Aotus nancymaae"                                           
#>  [663] "Aotus nancymai"                                            
#>  [664] "Astatotilapia calliptera"                                  
#>  [665] "Chromis callipterus"                                       
#>  [666] "Ctenochromis callipterus"                                  
#>  [667] "Haplochromis calliptera"                                   
#>  [668] "Haplochromis callipterus"                                  
#>  [669] "Rhamnus zizyphus"                                          
#>  [670] "Ziziphus jujuba"                                           
#>  [671] "Ailuropoda melanoleuca"                                    
#>  [672] "Micropterus dolomieu"                                      
#>  [673] "Micropterus velox"                                         
#>  [674] "Lycopersicon esculentum"                                   
#>  [675] "Lycopersicon esculentum_var._esculentum"                   
#>  [676] "Solanum esculentum"                                        
#>  [677] "Solanum lycopersicum"                                      
#>  [678] "Solanum lycopersicum_var._humboldtii"                      
#>  [679] "Poecilia mexicana"                                         
#>  [680] "Manis pentadactyla"                                        
#>  [681] "Meles meles"                                               
#>  [682] "Ursus meles"                                               
#>  [683] "Ornithorhynchus anatinus"                                  
#>  [684] "Platypus anatinus"                                         
#>  [685] "Felis uncia"                                               
#>  [686] "Panthera uncia"                                            
#>  [687] "Uncia uncia"                                               
#>  [688] "Alligator mississippiensis"                                
#>  [689] "Crocodilus mississipiensis"                                
#>  [690] "Myrmecophaga aculeata"                                     
#>  [691] "Tachyglossus aculeatus"                                    
#>  [692] "Colossoma macropomum"                                      
#>  [693] "Myletes macropomus"                                        
#>  [694] "Cordylus capensis"                                         
#>  [695] "Cordylus (Hemicordylus)_capensis"                          
#>  [696] "Hemicordylus capensis"                                     
#>  [697] "Pseudocordylus capensis"                                   
#>  [698] "Zonurus capensis"                                          
#>  [699] "Eptesicus fuscus"                                          
#>  [700] "Vespertilio fuscus"                                        
#>  [701] "Dromiciops australis"                                      
#>  [702] "Dromiciops gliroides"                                      
#>  [703] "Camelus pacos"                                             
#>  [704] "Lama guanicoe_pacos"                                       
#>  [705] "Lama pacos"                                                
#>  [706] "Vicugna pacos"                                             
#>  [707] "Mollienesia latipinna"                                     
#>  [708] "Poecilia latipinna"                                        
#>  [709] "Elephas maximus_indicus"                                   
#>  [710] "Corylus avellana"                                          
#>  [711] "Ostrea maxima"                                             
#>  [712] "Pecten maximus"                                            
#>  [713] "Felis viverrina"                                           
#>  [714] "Prionailurus viverrinus"                                   
#>  [715] "Gymnodraco acuticeps"                                      
#>  [716] "Thalarctos maritimus"                                      
#>  [717] "Ursus maritimus"                                           
#>  [718] "Lemur catta"                                               
#>  [719] "Myotis myotis"                                             
#>  [720] "Vespertilio myotis"                                        
#>  [721] "Lytechinus pictus"                                         
#>  [722] "Litopenaeus vannamei"                                      
#>  [723] "Penaeus (Litopenaeus)_vannamei"                            
#>  [724] "Penaeus vannamei"                                          
#>  [725] "Ursus arctos"                                              
#>  [726] "Vitis riparia"                                             
#>  [727] "Felis bengalensis"                                         
#>  [728] "Prionailurus bengalensis"                                  
#>  [729] "Clethrionomys glareolus"                                   
#>  [730] "Mus glareolus"                                             
#>  [731] "Myodes glareolus"                                          
#>  [732] "Mustela nigripes"                                          
#>  [733] "Putorius nigripes"                                         
#>  [734] "Pygocentrus nattereri"                                     
#>  [735] "Serrasalmus nattereri"                                     
#>  [736] "Alopex lagopus"                                            
#>  [737] "Canis lagopus"                                             
#>  [738] "Vulpes lagopus"                                            
#>  [739] "Cercocebus atys"                                           
#>  [740] "Cercocebus torquatus_atys"                                 
#>  [741] "Simia atys"                                                
#>  [742] "Lepidosiren annectens"                                     
#>  [743] "Protopterus annectens"                                     
#>  [744] "Rhinocryptis annectens"                                    
#>  [745] "Cerasus avium"                                             
#>  [746] "Prunus avium"                                              
#>  [747] "Prunus cerasus_var._avium"                                 
#>  [748] "Procambarus clarkii"                                       
#>  [749] "Sorex fumeus"                                              
#>  [750] "Macrorhinus angustirostris"                                
#>  [751] "Mirounga angustirostris"                                   
#>  [752] "Beta vulgaris_subsp._vulgaris"                             
#>  [753] "Beta vulgaris_subsp._vulgaris_var._altissima"              
#>  [754] "Beta vulgaris_Sugar_Beet_Group"                            
#>  [755] "Beta vulgaris_var._altissima"                              
#>  [756] "Eumetopias jubatus"                                        
#>  [757] "Phoca jubata"                                              
#>  [758] "Centruroides sculpturatus"                                 
#>  [759] "Diceros bicornis_minor"                                    
#>  [760] "Cicer arietinum"                                           
#>  [761] "Cleome hassleriana_Chodat,_1898"                           
#>  [762] "Tarenaya hassleriana"                                      
#>  [763] "Sebastes umbrosus"                                         
#>  [764] "Sebastichthys umbrosus"                                    
#>  [765] "Eriocheir chinensis"                                       
#>  [766] "Eriocheir japonica_sinensis"                               
#>  [767] "Eriocheir sinensis"                                        
#>  [768] "Dicentrarchus labrax"                                      
#>  [769] "Labrax labrax"                                             
#>  [770] "Morone labrax"                                             
#>  [771] "Perca labrax"                                              
#>  [772] "Roccus labrax"                                             
#>  [773] "Sciaena labrax"                                            
#>  [774] "Acanthopagrus latus"                                       
#>  [775] "Sparus latus"                                              
#>  [776] "Xiphophorus hellerii"                                      
#>  [777] "Xiphophorus helleri"                                       
#>  [778] "Acanthochromis polyacanthus"                               
#>  [779] "Acanthochromis polyacathus"                                
#>  [780] "Dascyllus polyacanthus"                                    
#>  [781] "Mustela vison"                                             
#>  [782] "Neogale vison"                                             
#>  [783] "Neovison vison"                                            
#>  [784] "Lingula anatina"                                           
#>  [785] "Lingula lingua"                                            
#>  [786] "Lingula nipponica"                                         
#>  [787] "Lingula unguis"                                            
#>  [788] "Madrepora faveolata"                                       
#>  [789] "Montastraea faveolata"                                     
#>  [790] "Montastrea faveolata"                                      
#>  [791] "Orbicella faveolata"                                       
#>  [792] "Chinchilla lanigera"                                       
#>  [793] "Chinchilla velligera"                                      
#>  [794] "Chinchilla villidera"                                      
#>  [795] "Mirounga leonina"                                          
#>  [796] "Phoca leonina"                                             
#>  [797] "Perognathus longimembris_pacificus"                        
#>  [798] "Cynocephalus variegatus"                                   
#>  [799] "Galeopithecus variegatus"                                  
#>  [800] "Galeopterus variegatus"                                    
#>  [801] "Vigna radiata"                                             
#>  [802] "Vitis vinifera"                                            
#>  [803] "Vitis vinifera_subsp._vinifera"                            
#>  [804] "Characodon multiradiatus"                                  
#>  [805] "Girardinichthys multiradiatus"                             
#>  [806] "Marmota flaviventris"                                      
#>  [807] "Phaseolus calcaratus"                                      
#>  [808] "Phaseolus chrysanthos"                                     
#>  [809] "Phaseolus chrysanthus"                                     
#>  [810] "Vigna calcarata"                                           
#>  [811] "Vigna umbellata"                                           
#>  [812] "Balaenoptera acutorostrata"                                
#>  [813] "Canis procyonoides"                                        
#>  [814] "Nyctereutes procyonoides"                                  
#>  [815] "Amphioxus floridae"                                        
#>  [816] "Branchiostoma floridae"                                    
#>  [817] "Moschus berezovskii"                                       
#>  [818] "Erythranthe guttata"                                       
#>  [819] "Mimulus guttatus_subsp._guttatus"                          
#>  [820] "Mimulus guttatus"                                          
#>  [821] "Camelus bactrianus"                                        
#>  [822] "Desmodus rotundus"                                         
#>  [823] "Phyllostoma rotundum"                                      
#>  [824] "Octopus sinensis"                                          
#>  [825] "Physeter catodon"                                          
#>  [826] "Physeter macrocephalus"                                    
#>  [827] "Alexandromys fortis"                                       
#>  [828] "Microtus fortis"                                           
#>  [829] "Apogon orbicularis"                                        
#>  [830] "Sphaeramia orbicularis"                                    
#>  [831] "Dendronephthya gigantea"                                   
#>  [832] "Canis hyaena"                                              
#>  [833] "Hyaena hyaena"                                             
#>  [834] "Helicophagus hypophthalmus"                                
#>  [835] "Pangasianodon hypophthalmus"                               
#>  [836] "Pangasius hypophthalmus"                                   
#>  [837] "Pangasius sutchi"                                          
#>  [838] "Castor canadensis"                                         
#>  [839] "Coelomys parahi"                                           
#>  [840] "Mus pahari"                                                
#>  [841] "Pseudochaenichthys georgianus"                             
#>  [842] "Capsella rubella"                                          
#>  [843] "Perkinsus marinus_ATCC_50983"                              
#>  [844] "Holocentrus leopardus"                                     
#>  [845] "Plectropomus leopardus"                                    
#>  [846] "Hippocampus zosterae"                                      
#>  [847] "Seriola dorsalis"                                          
#>  [848] "Seriola lalandi_dorsalis"                                  
#>  [849] "Felis canadensis"                                          
#>  [850] "Lynx canadensis"                                           
#>  [851] "Artibeus jamaicensis"                                      
#>  [852] "Citrus sinensis"                                           
#>  [853] "Citrus x_sinensis"                                         
#>  [854] "Punica granatum"                                           
#>  [855] "Abrus cyaneus"                                             
#>  [856] "Abrus precatorius"                                         
#>  [857] "Polypterus senegalus"                                      
#>  [858] "Acomys russatus"                                           
#>  [859] "Hemibagrus wyckioides"                                     
#>  [860] "Macrones wyckioides"                                       
#>  [861] "Mystus wyckioides"                                         
#>  [862] "Melanotaenia boesemani"                                    
#>  [863] "Sturnira hondurensis"                                      
#>  [864] "Amphilophus centrarchus"                                   
#>  [865] "Archocentrus centrarchus"                                  
#>  [866] "Cichlasoma centrarchus"                                    
#>  [867] "Heros centrarchus"                                         
#>  [868] "Delphinus melas"                                           
#>  [869] "Globicephala melaena"                                      
#>  [870] "Globicephala melas"                                        
#>  [871] "Manis javanica"                                            
#>  [872] "Phyllostomus hastatus"                                     
#>  [873] "Vespertilio hastatus"                                      
#>  [874] "Scyliorhinus canicula"                                     
#>  [875] "Silurana tropicalis"                                       
#>  [876] "Xenopus laevis_tropicalis"                                 
#>  [877] "Xenopus (Silurana)_tropicalis"                             
#>  [878] "Xenopus tropicalis"                                        
#>  [879] "Pipistrellus kuhlii"                                       
#>  [880] "Pipistrellus kuhli"                                        
#>  [881] "Vespertilio kuhlii"                                        
#>  [882] "Solea senegalensis"                                        
#>  [883] "Blennius fasciatus"                                        
#>  [884] "Salarias fasciatus"                                        
#>  [885] "Mugil cephalotus"                                          
#>  [886] "Mugil cephalus"                                            
#>  [887] "Mugil galapagensis"                                        
#>  [888] "Mugil japonicus"                                           
#>  [889] "Siphostoma scovelli"                                       
#>  [890] "Syngnathus scovelli"                                       
#>  [891] "Canis vulpes"                                              
#>  [892] "Vulpes vulpes"                                             
#>  [893] "Capra aegagrus_hircus"                                     
#>  [894] "Capra hircus"                                              
#>  [895] "Poeciliopsis prolifica"                                    
#>  [896] "Gopherus flavomarginatus"                                  
#>  [897] "Lontra canadensis"                                         
#>  [898] "Lutra canadensis"                                          
#>  [899] "Hesperomys torridus"                                       
#>  [900] "Onychomys torridus"                                        
#>  [901] "Elephas africanus"                                         
#>  [902] "Loxodonta africana_africana"                               
#>  [903] "Loxodonta africana"                                        
#>  [904] "Limia couchiana"                                           
#>  [905] "Xiphophorus couchianus"                                    
#>  [906] "Boophilus microplus"                                       
#>  [907] "Rhipicephalus (Boophilus)_microplus"                       
#>  [908] "Rhipicephalus microplus"                                   
#>  [909] "Betta splendens"                                           
#>  [910] "Molossus molossus"                                         
#>  [911] "Vespertilio molossus"                                      
#>  [912] "Lagenorhynchus obliquidens"                                
#>  [913] "Delphinus truncatus"                                       
#>  [914] "Tursiops truncatus"                                        
#>  [915] "Morone flavescens"                                         
#>  [916] "Perca flavescens"                                          
#>  [917] "Euarctos americanus"                                       
#>  [918] "Ursus americanus"                                          
#>  [919] "Arvicola nivalis"                                          
#>  [920] "Chionomys nivalis"                                         
#>  [921] "Microtus nivalis"                                          
#>  [922] "Felis rufus"                                               
#>  [923] "Lynx rufus"                                                
#>  [924] "Myotis brandtii"                                           
#>  [925] "Vespertilio brandtii"                                      
#>  [926] "Astatotilapia burtoni"                                     
#>  [927] "Chromis burtoni"                                           
#>  [928] "Haplochromis burtoni"                                      
#>  [929] "Sorex araneus"                                             
#>  [930] "Aplocheilus melastigmus"                                   
#>  [931] "Oryzias melastigma"                                        
#>  [932] "Silurus meridionalis"                                      
#>  [933] "Silurus soldatovi_meridionalis"                            
#>  [934] "Cucumis melo"                                              
#>  [935] "Hydra attenuata"                                           
#>  [936] "Hydra carnea"                                              
#>  [937] "Hydra littoralis"                                          
#>  [938] "Hydra magnipapillata"                                      
#>  [939] "Hydra vulgaris"                                            
#>  [940] "Anoplopoma fimbria"                                        
#>  [941] "Gadus fimbria"                                             
#>  [942] "Alosa alosa"                                               
#>  [943] "Clupea alosa"                                              
#>  [944] "Chelonia mydas"                                            
#>  [945] "Testudo mydas"                                             
#>  [946] "Ctenocephalides felis"                                     
#>  [947] "Brienomyrus kingsleyae"                                    
#>  [948] "Brienomyrus sp._CAB"                                       
#>  [949] "Mormyrus kingsleyae"                                       
#>  [950] "Paramormyrops kingsleyae"                                  
#>  [951] "Pollimyrus kingsleyae"                                     
#>  [952] "Stylophora pistillata"                                     
#>  [953] "Cyrtodiopsis dalmanii"                                     
#>  [954] "Diopsis dalmanni"                                          
#>  [955] "Teleopsis dalmanni"                                        
#>  [956] "Rhagoletis zephyria"                                       
#>  [957] "Rhodamnia argentea"                                        
#>  [958] "Gasterosteus aculeatus"                                    
#>  [959] "Labrus celidotus"                                          
#>  [960] "Notolabrus celidotus"                                      
#>  [961] "Budorcas taxicolor"                                        
#>  [962] "Nelumbo nucifera"                                          
#>  [963] "Amphiprion ocellaris"                                      
#>  [964] "Arvicola amphibius"                                        
#>  [965] "Arvicola terrestris_(Linnaeus,_1758)"                      
#>  [966] "Mus amphibius"                                             
#>  [967] "Daphnia magna"                                             
#>  [968] "Phaseolus vulgaris"                                        
#>  [969] "Psammomys obesus"                                          
#>  [970] "Carlito syrichta"                                          
#>  [971] "Simia syrichta"                                            
#>  [972] "Tarsius syrichta"                                          
#>  [973] "Cyprinodon tularosa"                                       
#>  [974] "Gouania willdenowi"                                        
#>  [975] "Lepadogaster willdenowi"                                   
#>  [976] "Ochotona princeps"                                         
#>  [977] "Phytophthora sojae"                                        
#>  [978] "Equus caballus_przewalskii"                                
#>  [979] "Equus ferus_przewalskii"                                   
#>  [980] "Equus przewalskii"                                         
#>  [981] "Phoca vitulina"                                            
#>  [982] "Coecilia bivitatum"                                        
#>  [983] "Rhinatrema bivitattum"                                     
#>  [984] "Rhinatrema bivittatum"                                     
#>  [985] "Gambusia affinis"                                          
#>  [986] "Heterandria affinis"                                       
#>  [987] "Lagomys curzoniae"                                         
#>  [988] "Ochotona curzonae"                                         
#>  [989] "Ochotona curzoniae"                                        
#>  [990] "Kogia breviceps"                                           
#>  [991] "Physeter breviceps"                                        
#>  [992] "Ambassis ranga"                                            
#>  [993] "Chanda ranga"                                              
#>  [994] "Parambassis ranga"                                         
#>  [995] "Pseudambassis ranga"                                       
#>  [996] "Clupea cyprinoides"                                        
#>  [997] "Megalops cyprinoides"                                      
#>  [998] "Diospyros lotus"                                           
#>  [999] "Hippoglossus stenolepis"                                   
#> [1000] "Phacochoerus africanus"                                    
#> [1001] "Corythoichthys intestinalis"                               
#> [1002] "Syngnatus intestinalis"                                    
#> [1003] "Mandrillus leucophaeus"                                    
#> [1004] "Papio leucophaeus"                                         
#> [1005] "Simia leucophaea"                                          
#> [1006] "Epinephelus fuscoguttatus"                                 
#> [1007] "Perca summana_fuscoguttata"                                
#> [1008] "Asterina miniata"                                          
#> [1009] "Patiria miniata"                                           
#> [1010] "Rhinolophus rouxii_sinicus"                                
#> [1011] "Rhinolophus sinicus"                                       
#> [1012] "Lampris incognitus"                                        
#> [1013] "Monachus schauinslandi"                                    
#> [1014] "Neomonachus schauinslandi"                                 
#> [1015] "Hippoglossus hippoglossus"                                 
#> [1016] "Pleuronectes hippoglossus"                                 
#> [1017] "Andrographis paniculata"                                   
#> [1018] "Etheostoma cragini"                                        
#> [1019] "Perca chuatsi"                                             
#> [1020] "Siniperca chuatsi"                                         
#> [1021] "Meriones unguiculatus"                                     
#> [1022] "Colobus angolensis_palliatus"                              
#> [1023] "Notothenia coriiceps"                                      
#> [1024] "Hypomesus transpacificus"                                  
#> [1025] "Dermochelys coriacea"                                      
#> [1026] "Testudo coriacea"                                          
#> [1027] "Bufo bufo_gargarizans"                                     
#> [1028] "Bufo gargarizans"                                          
#> [1029] "Bufo japonicus_gargarizans"                                
#> [1030] "Delphinapterus leucas"                                     
#> [1031] "Delphinus leucas"                                          
#> [1032] "Fugu flavidus"                                             
#> [1033] "Takifugu flavidus"                                         
#> [1034] "Pteronotus mesoamericanus"                                 
#> [1035] "Pteronotus parnellii_mesoamericanus"                       
#> [1036] "Citrus clementina"                                         
#> [1037] "Citrus deliciosa_x_Citrus_sinensis"                        
#> [1038] "Fugu rubripes"                                             
#> [1039] "Sphaeroides rubripes"                                      
#> [1040] "Takifugu rubripes"                                         
#> [1041] "Tetraodon rubripes"                                        
#> [1042] "Homarus americanus"                                        
#> [1043] "Osteoglossum formosum"                                     
#> [1044] "Scleropages formosus"                                      
#> [1045] "Larimichthys crocea"                                       
#> [1046] "Pseudosciaena amblyceps"                                   
#> [1047] "Pseudosciaena crocea"                                      
#> [1048] "Sciaena crocea"                                            
#> [1049] "Fragaria vesca"                                            
#> [1050] "Folsomia candida"                                          
#> [1051] "Limulus polyphemus"                                        
#> [1052] "Doryrhamphus dactyliophorus"                               
#> [1053] "Dunckerocampus dactyliophorus"                             
#> [1054] "Syngnathus dactyliophorus"                                 
#> [1055] "Epinephelus lanceolatus"                                   
#> [1056] "Holocentrus lanceolatus"                                   
#> [1057] "Promicrops lanceolatus"                                    
#> [1058] "Mizuhopecten yessoensis"                                   
#> [1059] "Patinopecten yessoensis"                                   
#> [1060] "Patiopecten yessoensis"                                    
#> [1061] "Pecten yessoensis"                                         
#> [1062] "Calamoichthys calabaricus"                                 
#> [1063] "Erpetoichthys calabaricus"                                 
#> [1064] "Platypoecilus maculatus"                                   
#> [1065] "Xiphophorus maculatus"                                     
#> [1066] "Echeneis naucrates"                                        
#> [1067] "Triplophysa rosa"                                          
#> [1068] "Antechinus flavipes"                                       
#> [1069] "Phascogale flavipes"                                       
#> [1070] "Balaena musculus"                                          
#> [1071] "Balaenoptera musculus"                                     
#> [1072] "Rhinolophus ferrumequinum"                                 
#> [1073] "Vespertilio ferrumequinum"                                 
#> [1074] "Oryza brachyantha"                                         
#> [1075] "Chrysemys picta"                                           
#> [1076] "Testudo picta"                                             
#> [1077] "Trachemys picta"                                           
#> [1078] "Tetrahymena thermophila_SB210"                             
#> [1079] "Myripristis murdjan"                                       
#> [1080] "Ostichthys murdjan"                                        
#> [1081] "Perca murdjan"                                             
#> [1082] "Sciaena murdjan"                                           
#> [1083] "Amphiprion testudineus"                                    
#> [1084] "Anabas testudineus"                                        
#> [1085] "Anthias testudineus"                                       
#> [1086] "Antias testudineus"                                        
#> [1087] "Amygdalus communis"                                        
#> [1088] "Prunus amygdalus"                                          
#> [1089] "Prunus communis"                                           
#> [1090] "Prunus dulcis"                                             
#> [1091] "Prunus dulcis_var._sativa"                                 
#> [1092] "Oryzias latipes"                                           
#> [1093] "Poecilia latipes"                                          
#> [1094] "Sarcophilus harrisii"                                      
#> [1095] "Sarcophilus laniarius_(Owen,_1838)"                        
#> [1096] "Sarcophilus laniarius"                                     
#> [1097] "Ursinus harrisii"                                          
#> [1098] "Ictalurus furcatus"                                        
#> [1099] "Pimelodus furcatus"                                        
#> [1100] "Branchiostoma belcheri"                                    
#> [1101] "Gigantopelta aegis"                                        
#> [1102] "Lytechinus variegatus"                                     
#> [1103] "Diaphorina citri"                                          
#> [1104] "Epinephelus moara"                                         
#> [1105] "Serranus moara"                                            
#> [1106] "Stegodyphus dumicola"                                      
#> [1107] "Boleophthalmus pectinirostris"                             
#> [1108] "Gobius pectinirostris"                                     
#> [1109] "Lacerrta muralis"                                          
#> [1110] "Podarcis muralis"                                          
#> [1111] "Seps muralis"                                              
#> [1112] "Austrofundulus limnaeus"                                   
#> [1113] "Columba livia_domestica"                                   
#> [1114] "Columba livia"                                             
#> [1115] "Citellus parryii"                                          
#> [1116] "Spermophilus parryii"                                      
#> [1117] "Spermophilus parryi"                                       
#> [1118] "Urocitellus parryii"                                       
#> [1119] "Latimeria chalumnae"                                       
#> [1120] "Pleuronectes maximus"                                      
#> [1121] "Psetta maxima"                                             
#> [1122] "Rhombus maximus"                                           
#> [1123] "Scophthalmus maximus"                                      
#> [1124] "Sesamum indicum"                                           
#> [1125] "Sesamum orientale"                                         
#> [1126] "Cyclopterus lumpus"                                        
#> [1127] "Armeniaca mume"                                            
#> [1128] "Prunus mume"                                               
#> [1129] "Myotis davidii"                                            
#> [1130] "Vespertilio Davidii"                                       
#> [1131] "Didelphys agilis"                                          
#> [1132] "Gracilinanus agilis"                                       
#> [1133] "Phocoena sinus"                                            
#> [1134] "Acanthophacelus reticulata"                                
#> [1135] "Poecilia (Acanthophacelus)_reticulata"                     
#> [1136] "Poecilia latipinna_reticulata"                             
#> [1137] "Poecilia reticulata"                                       
#> [1138] "Gopherus evgoodei"                                         
#> [1139] "Australorbis glabratus"                                    
#> [1140] "Biomphalaria glabrata"