Abbreviation,Species,Higher rank,Lower rank,Genome version,Link to genome data
Acal,Aplysia californica,Mollusca,Gastropoda,0.0,http://www.broadinstitute.org/ftp/pub/assemblies/invertebrates/aplysia/AplCal3/A_californica_v0.assembly.fasta.gz
Acas,Acanthamoeba castellanii,Amoebozoa,Acanthamoebidae,2010210,ftp://ftp.hgsc.bcm.edu/AcastellaniNeff/Acas20100210/LinearScaffolds/Acas20100210.contigs.agp.linear.fa
Agam,Anopheles gambiae,Arthropoda,Insecta,4.2,http://genome.wustl.edu/pub/organism/Invertebrates/Anopheles_gambiae/assembly/Anopheles_gambiae_S-4.2/output/supercontigs.fa.gz
Alyr,Arabidopsis lyrata,Plantae,Angiosperms,107,ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Alyrata/assembly/Alyrata_107.fa.gz
Asuu,Ascaris suum,Nematoda,Ascaridomorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/a_suum/sequence/genomic/a_suum.PRJNA62057.WS238.genomic.fa.gz
Ath,Arabidopsis thaliana,Plantae,Angiosperms,TAIR10,ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/
Avit,Acanthocheilonema viteae,Nematoda,Spiruromorpha,1.0,http://acanthocheilonema.nematod.es
Bmal,Brugia malayi,Nematoda,Spiruromorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/b_malayi/sequence/genomic/b_malayi.PRJNA10729.WS238.genomic.fa.gz
briC,Caenorhabditis briggsae,Nematoda,Rhabditomorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/c_briggsae/sequence/genomic/c_briggsae.PRJNA10731.WS238.genomic.fa.gz
Bxyl,Bursaphelenchus xylophilus,Nematoda,Tylenchomorpha,1.2,ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BurXv1.2.supercontigs.fa.gz
C11sp,Caenorhabditis sp11,Nematoda,Rhabditomorpha,3.0.1,http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_sp11_JU1373/assembly/Caenorhabditis_sp11_JU1373-3.0.1/output/supercontigs.fa.gz
C5sp,Caenorhabditis sp. 5,Nematoda,Rhabditomorpha,WS230,ftp://ftp.wormbase.org/pub/wormbase/releases/WS230/species/c_sp5/c_sp5.WS230.genomic.fa.gz
Cang,Caenorhabditis angaria,Nematoda,Rhabditomorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/c_angaria/sequence/genomic/c_angaria.PRJNA51225.WS238.genomic.fa.gz
Cbre,Caenorhabditis brenneri,Nematoda,Rhabditomorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/c_brenneri/sequence/genomic/c_brenneri.PRJNA20035.WS238.genomic.fa.gz
Cele,Caenorhabditis elegans,Nematoda,Rhabditomorpha,WS235,ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/sequence/genomic/c_elegans.WS235.genomic.fa.gz
Cjap,Caenorhabditis japonica,Nematoda,Rhabditomorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/c_japonica/sequence/genomic/c_japonica.PRJNA12591.WS238.genomic.fa.gz
Crem,Caenorhabditis remanei,Nematoda,Rhabditomorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/c_remanei/sequence/genomic/c_remanei.PRJNA53967.WS238.genomic.fa.gz
Dimm,Dirofilaria immitis,Nematoda,Spiruromorpha,2.2,http://dirofilaria.nematod.es
Dpul,Daphnia pulex,Arthropoda,Crustacea,1.0,http://genome.jgi.doe.gov/Dappu1/download/Daphnia_pulex.fasta.gz
Dsim,Drosophila simulans,Arthropoda,Insecta,1.4,ftp://ftp.flybase.net/genomes/Drosophila_simulans/dsim_r1.4_FB2012_03/fasta/dsim-all-chromosome-r1.4.fasta.gz
Dviv,Dictyocaulus viviparus,Nematoda,Rhabditomorpha,1.0,http://dictyocaulus.nematod.es
Ebre,Enoplus brevis,Nematoda,Enoplida,1.1,http://enoplus.nematod.es
Gpal,Globodera pallida,Nematoda,Tylenchomorpha,30052012,ftp://ftp.sanger.ac.uk/pub/pathogens/Globodera/pallida/Assembly/ARCHIVE/Gpal.genome.30052012.scaffolds.fa.gz
Haor,Howardula aoronymphium,Nematoda,Tylenchomorpha,1.0,http://nematodes.org/downloads/959nematodegenomes/blast/db/Howardula_aoronymphium_clc_1.fna
Hbac,Heterorhabditis bacteriophora,Nematoda,Rhabditomorpha,1.2.1,http://genome.wustl.edu/pub/organism/Invertebrates/Heterorhabditis_bacteriophora/assembly/Heterorhabditis_bacteriophora-1.2.1/output/contigs.fa.gz
Hcon,Haemonchus contortus,Nematoda,Rhabditomorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/h_contortus/sequence/genomic/h_contortus.PRJEB506.WS238.genomic.fa.gz
Hduj,Hypsibius dujardini,Tardigrada,Eutardigrada,2.3,http://badger.bio.ed.ac.uk/H_dujardini/fileDownload/zip_download?fileName=nHd.2.3.abv500.fna
Lgi,Lottia gigantea,Mollusca,Gastropoda,1.0,ftp://ftp.jgi-psf.org/pub/JGI_data/Lottia_gigantea/v1.0/Lotgi1_assembly_scaffolds.fasta.gz
Lloa,Loa loa,Nematoda,Spiruromorpha,3.0,http://www.broadinstitute.org/annotation/genome/filarial_worms/download/?sp=EASupercontigsFasta&sp=SLoa_loa_V3&sp=S.zip
Lsig,Litomosoides sigmodontis,Nematoda,Spiruromorpha,2.2,http://litomosoides.nematod.es
Mflo,Meloidogyne floridensis,Nematoda,Tylenchomorpha,1.0,http://meloidogyne.nematod.es
Mhap,Meloidogyne hapla,Nematoda,Tylenchomorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/m_hapla/sequence/genomic/m_hapla.PRJNA29083.WS238.genomic.fa.gz
Minc,Meloidogyne incognita,Nematoda,Tylenchomorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/m_incognita/sequence/genomic/m_incognita.PRJEA28837.WS238.genomic.fa.gz
Nve,Nematostella vectensis,Cnidaria,Anthozoa,1.0,ftp://ftp.jgi-psf.org/pub/JGI_data/Nematostella_vectensis/v1.0/assembly/Nemve1.fasta.gz
Nvi,Nasonia vitripennis,Arthropoda,Insecta,2.0,ftp://ftp.hgsc.bcm.edu/Nvitripennis/fasta/Nvit_2.0/linearScaffolds/Nvit_2.0.linear.fa.gz
Ooch,Onchocerca ochengi,Nematoda,Spiruromorpha,2.0,http://onchocerca.nematod.es
Otip,Oscheius tipulae,Nematoda,Rhabditomorpha,3.1,http://nematodes.org/downloads/959nematodegenomes/blast/db/Oscheius_tipulae_clc3_1.fna
Ovol,Onchocerca volvulus,Nematoda,Spiruromorpha,1.0,http://www.broadinstitute.org/annotation/genome/filarial_worms/download/?sp=EASupercontigsFasta&sp=SOnchocerca_volvulus_V1&sp=S.zip
Ppac,Pristionchus pacificus,Nematoda,Diplogasteromorpha,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/p_pacificus/sequence/genomic/p_pacificus.PRJNA12644.WS238.genomic.fa.gz
Pred,Panagrellus redivivus,Nematoda,Panagrolaimomorpha,1.0,http://www.ncbi.nlm.nih.gov/nuccore?term=KB454917:KB455574[PACC]
Rcul,Romanomermis culicivorax,Nematoda,Mermithida,1.0,http://romanomermis.nematod.es
Srat,Strongyloides ratti,Nematoda,Panagrolaimomorpha,4.0,ftp://ftp.sanger.ac.uk/pub/pathogens/Strongyloides/ratti/version_4/Sratti_v4.genome.fa
Tmur,Trichuris muris,Nematoda,Trichinellida,2b,ftp://ftp.sanger.ac.uk/pub/pathogens/Trichuris/muris/genome/version_2b/Tmuris_v2b.genome_scaffolds.fa
Tspi,Trichinella spiralis,Nematoda,Trichinellida,WS238,ftp://ftp.wormbase.org/pub/wormbase/species/t_spiralis/sequence/genomic/t_spiralis.PRJNA12603.WS238.genomic.fa.gz
Vcar,Volvox carteri,Plantae,Chlorophyta,9.0,ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Vcarteri/assembly/Vcarteri_199.fa.gz
Wban,Wuchereria bancrofti,Nematoda,Spiruromorpha,1.0,http://www.broadinstitute.org/annotation/genome/filarial_worms/download/?sp=EASupercontigsFasta&sp=SWuchereria_bancrofti_V1&sp=S.zip
,Other reference data,,,,
PAT,Pristionchus pacificus Pat1-like,Reference,Reference,,"Mathieu Piednoël, personal communication"
BAS,RepBase_Crypton,Reference,Reference,,http://www.girinst.org/protected/repbase_extract.php?division=&customdivision=&rank=&type=Crypton&autonomous=1&nonautonomous=&simple=1&format=EMBL&sa=Download
BAS,RepBase_DIRS,Reference,Reference,,http://www.girinst.org/protected/repbase_extract.php?division=&customdivision=&rank=&type=DIRS&autonomous=1&nonautonomous=&simple=1&format=EMBL&sa=Download
RET,Retrobase DIRS,Reference,Reference,,http://biocadmin.otago.ac.nz/fmi/xsl/retrobase/type1.xsl?-db=retrobase.fp7&-lay=AllFieldsLayout&-max=all&-sortfield.1=Subtype&-sortfield.2=Type&-sortfield.3=Family&Format=Method&-find