Order of Species in Eukaryote Phylogeny Species File Name Source_Part1 Source_Part2 1 H.sapiens.fa hg19 from ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/ 2 P.troglodytes.fa chromosomes from http://genome.wustl.edu/pub/organism/Primates/Pan_troglodytes/assembly/Pan_troglodytes-2.1/output/chromosomes 3 P.pygmaeus.fa chromosomes from ftp://hgdownload.cse.ucsc.edu/goldenPath/ponAbe2/bigZips/ 4 M.mulatta.fa supercontigs from http://genome.wustl.edu/pub/organism/Primates/Macaca_mulatta/assembly/Macaca_mulatta-1.0/ 5 M.musculus.fa genome from ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/ 6 R.norvegicus.fa chromosomes from ftp://hgdownload.cse.ucsc.edu/goldenPath/rn4/bigZips/ 7 C.porcellus.fa from ftp://hgdownload.cse.ucsc.edu/goldenPath/cavPor3/bigZips/ 8 C.familiaris.fa chromosomes from ftp://hgdownload.cse.ucsc.edu/goldenPath/canFam2/chromosomes/ 9 E.caballus.fa chromosomes from ftp://hgdownload.cse.ucsc.edu/goldenPath/equCab2/chromosomes/ 10 B.taurus.fa chromosomes (v4.0) from ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/chromosomes/ 11 M.domestica.fa chromosomes from ftp://hgdownload.cse.ucsc.edu/goldenPath/monDom5/bigZips/ 12 O.anatinus.fa chromosomes from ftp://ftp.ensembl.org/pub/release-52/fasta/ornithorhynchus_anatinus/dna/ 13 G.gallus.fa supercontigs from http://genome.wustl.edu/pub/organism/Other_Vertebrates/Gallus_gallus/assembly/Gallus_gallus-3.0/output/ 14 X.tropicalis.fa unmasked assembled scaffolds v4.1 from http://genome.jgi-psf.org/Xentr4/Xentr4.download.ftp.html 15 T.rubripes.fa chromosomes from ftp://hgdownload.cse.ucsc.edu/goldenPath/fr2/ 16 T.nigroviridis.fa genome from ftp://ftp.ncbi.nih.gov/genbank/wgs/wgs.CAAE.gbff.gz 17 G.aculeatus.fa chromosomes from ftp://hgdownload.cse.ucsc.edu/goldenPath/gasAcu1/bigZips/ 18 O.latipes.fa from ftp://hgdownload.cse.ucsc.edu/goldenPath/oryLat2/bigZips/ 19 D.rerio.fa chromosomes from ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer6/chromosomes/ 20 C.savignyi.fa from http://mendel.stanford.edu/SidowLab/ciona.html 21 C.intestinalis.fa unmasked assembly from http://genome.jgi-psf.org/Cioin2/Cioin2.download.ftp.html 22 S.purpuratus.fa chromosomes from ftp://hgdownload.cse.ucsc.edu/goldenPath/strPur2/bigZips/ 23 B.floridae.fa unmasked assembly from http://genome.jgi-psf.org/Brafl1/Brafl1.download.ftp.html 24 N.vectensis.fa unmasked scaffolds from http://genome.jgi-psf.org/Nemve1/Nemve1.download.ftp.html 25 T.adhaerens.fa unmasked assembly from http://genome.jgi-psf.org/Triad1/Triad1.download.ftp.html 26 C.spI.fa unmasked assembly from http://genome.jgi-psf.org/Capca1/Capca1.download.ftp.html 27 H.robusta.fa unmasked assembly from http://genome.jgi-psf.org/Helro1/Helro1.download.ftp.html 28 L.gigantea.fa unmasked assembly from http://genome.jgi-psf.org/Lotgi1/Lotgi1.download.ftp.html 29 D.melanogaster.fa chromosomes from FlyBase 30 D.ananassae.fa chromosomes from FlyBase 31 D.pseudoobscura.fa chromosomes from FlyBase 32 D.willistoni.fa chromosomes from FlyBase 33 D.virilis.fa chromosomes from FlyBase 34 D.mojavensis.fa chromosomes from FlyBase 35 D.grimshawi.fa chromosomes from FlyBase 36 A.aegypti.fa supercontigs from http://www.broadinstitute.org/annotation/genome/aedes_aegypti.2/MultiDownloads.html 37 C.pipiens.fa supercontigs from http://www.broadinstitute.org/annotation/genome/culex_pipiens/MultiDownloads.html 38 A.gambiae.fa supercontigs from http://genome.wustl.edu/pub/organism/Invertebrates/Anopheles_gambiae/assembly/Anopheles_gambiae_M-3.0/output/ 39 B.mori.fa genome from ftp://silkdb.org/pub/current/Genome/ 40 T.castaneum.fa contigs from ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Tcastaneum/Tcas3.0/ 41 N.vitripennis.fa scaffolds from ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Nvitripennis/fasta/Nvit_2.0/linearScaffolds/ 42 A.mellifera.fa assembled chromosomes from ftp://ftp.ncbi.nih.gov/genomes/Apis_mellifera/Assembled_chromosomes/ 43 A.pisum.fa scaffolds from http://genouest.org/AphidBase 44 P.humanus.fa supercontigs from http://phumanus.vectorbase.org/GetData/Downloads?type=Genome 45 D.pulex.fa scaffolds from http://genome.jgi-psf.org/Dappu1/Dappu1.download.ftp.html 46 I.scapularis.fa supercontigs from http://www.vectorbase.org/GetData/Downloads/ 47 C.briggsae.fa chromosomes from http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_briggsae/assembly/Caenorhabditis_briggsae-1.0/output/chromosomes/ 48 C.remanei.fa supercontigs from http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_remanei/assembly/Caenorhabditis_remanei-15.0.1/output/ 49 C.elegans.fa WS216 from ftp://ftp.wormbase.org/pub/wormbase/genomes/c_elegans/sequences/dna/ 50 C.brenneri.fa supercontigs from http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_PB2801/assembly/Caenorhabditis_PB2801-6.0.1/output/ 51 C.japonica.fa supercontigs from http://genome.wustl.edu/pub/organism/Invertebrates/Caenorhabditis_japonica/assembly/Caenorhabditis_japonica-4.0.1/output/ 52 P.pacificus.fa supercontigs from http://genome.wustl.edu/pub/organism/Invertebrates/Pristionchus_pacificus/assembly/Pristionchus_pacificus-5.0.1/output/ 53 B.malayi.fa WS216 from ftp://ftp.wormbase.org/pub/wormbase/genomes/b_malayi/sequences/dna/ 54 S.mansoni.fa supercontigs from ftp://ftp.sanger.ac.uk/pub/pathogens/Schistosoma/mansoni/genome/Assembly-v3.1/ 55 M.brevicollis.fa unmasked assembly from http://genome.jgi-psf.org/Monbr1/Monbr1.download.ftp.html 56 S.cerevisiae.fa SGD "October, 2008 > downloaded from SGD" 57 C.glabrata.fa Genolevures "October, 2008 > downloaded from Genolevures" 58 K.lactis.fa Genolevures "October, 2008 > downloaded from Genolevures" 59 C.albicans.fa CGD "November, 2008 > downloade from http://www.candidagenome.org/download/sequence/Assembly21/current/" 60 D.hansenii.fa Genolevures "October, 2008 > downloaded from Genolevures" 61 Y.lipolytica.fa Genolevures "October, 2008 > downloaded from Genolevures" 62 A.fumigatus.fa supercontigs from http://www.broadinstitute.org/annotation/genome/aspergillus_group/MultiDownloads.html 63 C.immitis.fa supercontigs from http://www.broadinstitute.org/annotation/genome/coccidioides_group/MultiDownloads.html 64 S.nodorum.fa supercontigs from http://www.broadinstitute.org/annotation/genome/stagonospora_nodorum.2/MultiDownloads.html 65 S.sclerotiorum.fa supercontigs from http://www.broadinstitute.org/annotation/genome/sclerotinia_sclerotiorum/MultiDownloads.html 66 F.graminearum.fa supercontigs (no mito) from http://www.broadinstitute.org/annotation/genome/fusarium_graminearum/MultiDownloads.html 67 N.crassa.fa Broad Fungal Genome Initiative "October, 2008 > downloaded supercontigs file from Broad" 68 M.grisea.fa genome from http://www.broadinstitute.org/cgi-bin/annotation/magnaporthe/download_license.cgi 69 S.pombe.fa Gene DB "October, 2008 > downloaded from ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/" 70 C.neoformans.fa scaffolds from http://www-sequence.stanford.edu/group/C.neoformans/download.html 71 C.cinereus.fa supercontigs from http://www.broadinstitute.org/annotation/genome/coprinus_cinereus/MultiDownloads.html 72 U.maydis.fa contigs from http://www.broadinstitute.org/annotation/genome/ustilago_maydis.2/MultiDownloads.html 73 P.graminis.fa unmasked assembly from http://genome.jgi-psf.org/Pucgr1/Pucgr1.download.ftp.html 74 R.oryzae.fa supercontigs from http://www.broadinstitute.org/annotation/genome/rhizopus_oryzae/MultiDownloads.html 75 B.dendrobatidis.fa supercontigs (no mitochondrion) from http://www.broadinstitute.org/annotation/genome/batrachochytrium_dendrobatidis/MultiDownloads.html 76 D.discoideum.fa from http://dictybase.org/db/cgi-bin/dictyBase/download/download.pl?area=blast_databases&ID=dicty_primary_genomic.gz 77 S.bicolor.fa unmasked assembly from http://genome.jgi-psf.org/Sorbi1/Sorbi1.download.ftp.html 78 O.sativa.fa "genome file ""all.con"" from ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_6.1/all.dir/" 79 A.thaliana.fa genome from http://www.plantgdb.org/XGDB/phplib/download.php?GDB=At 80 P.trichocarpa.fa unmasked assembly from ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v5.0/Ptrichocarpa/assembly/ 81 P.patens.fa unmasked assembly from http://genome.jgi-psf.org/physcomitrella/physcomitrella.download.ftp.html 82 C.reinhardtii.fa scaffolds v4 from http://genome.jgi-psf.org/Chlre4/Chlre4.download.ftp.html 83 O.tauri.fa unmasked assembly from http://genome.jgi-psf.org/Ostta4/Ostta4.download.ftp.html 84 P.sojae.fa unmasked assembly from http://genome.jgi-psf.org/Physo1_1/Physo1_1.download.ftp.html 85 P.ramorum.fa unmasked assembly from http://genome.jgi-psf.org/Phyra1_1/Phyra1_1.download.ftp.html 86 T.pseudonana.fa mapped chromosomes and unmapped scaffolds from http://genome.jgi-psf.org/Thaps3/Thaps3.download.ftp.html 87 C.merolae.fa chromosomes from http://merolae.biol.s.u-tokyo.ac.jp/download/ 88 T.parva.fa genome from http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide&cmd=Search&term=AAGK01000001:AAGK01000009[PACC] 89 T.annulata.fa "NT_167255, NC_011099, NC_011129, NC_011100, NC_011098 downloaded from GenBank" 90 P.vivax.fa downloaded contigs as one fasta file from http://www.ncbi.nlm.nih.gov/sites/entrez?db=Nucleotide&cmd=Search&term=AAKM01000001:AAKM01002770[PACC] 91 P.falciparum.fa chromosomes from ftp://ftp.sanger.ac.uk/pub/pathogens/Plasmodium/falciparum/3D7/genome.20090811/ 92 C.hominis.fa scaffolds from http://cryptodb.org/common/downloads/release-4.3/Chominis/ 93 C.parvum.fa scaffolds from http://cryptodb.org/common/downloads/release-4.3/Cparvum/ 94 T.thermophila.fa genome from ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/t_thermophila/annotation_dbs/final_release_oct2008/ 95 T.vaginalis.fa genome from http://trichdb.org/common/downloads/release-1.2/ 96 E.histolytica.fa contigs from ftp://ftp.sanger.ac.uk/pub/pathogens/E_histolytica/WGS_ASSEMBLY/ 97 L.major.fa genome from ftp://ftp.sanger.ac.uk/pub/databases/L.major_sequences/DATASETS/ 98 T.cruzi.fa esmeraldo-like sequence from http://tritrypdb.org/common/downloads/release-2.3/Tcruzi/ 99 G.lamblia.fa scaffolds from http://giardiadb.org/common/downloads/release-2.2/GintestinalisAssemblageE/ NA E.coliK12.fa downloaded from NCBI (accession NC_000913.2)