This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/ce11/multiz135way/README.txt This directory contains compressed multiple alignments of the following assemblies to the C. elegans genome (ce11, Feb. 2013): These alignments were prepared using the methods described in the track description file: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce11&g=cons135way based on the phylogenetic tree: ce11.135way.nh. Files in this directory: - ce11.135way.nh - phylogenetic tree used during the multiz multiple alignment, using the UCSC database name, or sequence name for those sequences that are not hosted in UCSC databases. - ce11.135way.scientificName.nh - same as ce11.135way.nh with the sequence name replaced with the scientific name for the species. - ce11.135way.taxId.nh - same as ce11.135way.nh with the sequence name replaced with the NCBI taxonomy identification. *** NOTE *** This phylogenetic tree was derived from kmers in common counting between the sequences to obtain a 'distance' matrix, then using the phylip command 'neighbors' operation for the simple neighbor joining algorithm to establish this binary tree. This tree is not necessarily biologically correct, but it does serve as a useful guide tree for the multiz alignment procedure. - nameCrossReference.txt - tab separated columns with the different names - for these sequences and databases, columns: 1. sequence name - UCSC database or scientific name - sequence names used in MAF files 2. NCBI accession 3. NCBI taxon identifier 4. assembly name 5. scientific name - sequences - directory of all sequence used for these alignments when the sequence is not in a UCSC database/browser. - upstream*.ensGene..maf.gz - alignments of regions upstream of Ensembl genes - chr*.maf.gz - the multiple alignments on C. elegans for each chromosome - md5sum.txt - md5 check sums of these files to verify correct download files The "alignments" directory contains compressed FASTA alignments for the CDS regions for three gene tracks, ws245Genes, refGene, ensGene, of the C. elegans genome (ce11, Feb. 2013) aligned to the assemblies. The chr*.maf.gz files contain all the alignments for the chromosomes in the C. elegans genome, including additional annotations to indicate gap context and genomic breaks for the sequence in the underlying genome assemblies. Note, the compressed data size of these maf files is 4 Gb, uncompressed is approximately 50 Gb. The upstream*.*.maf.gz files contain alignments in regions upstream of annotated transcription starts for Ensembl genes. with annotated 5' UTRs. These files differ from the standard MAF format: they display alignments that extend from start to end of the upstream region in C. elegans, whether or not alignments actually exist. In situations where no alignments exist or the alignments of one or more species are missing, dot (".") is used as a placeholder. Multiple regions of an assembly's sequence may align to a single region in C. elegans; therefore, only the species name is displayed in the alignment data and no position information is recorded. The alignment score is always zero in these files. For a description of multiple alignment format (MAF), see http://genome.ucsc.edu/goldenPath/help/maf.html. PhastCons conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/ce11/phastCons135way PhyloP conservation scores for these alignments are available at: http://hgdownload.cse.ucsc.edu/goldenPath/ce11/phyloP135way --------------------------------------------------------------- Assemblies used in these alignments: C. elegans - Caenorhabditis elegans Feb. 2013 (WBcel235/ce11) (reference) A. ceylanicum - Ancylostoma ceylanicum Mar. 2014 (WS243/Acey_2013.11.30.genDNA/ancCey1) (net) Acrobeloides_nanus - Acrobeloides nanus UNIVERSITY COLLEGE LONDON Jun. 2018 - GCA_900406225.1 - v1 (net) Ancylostoma_caninum - Ancylostoma caninum The Genome Institute Jul. 2018 - GCA_003336725.1 - A_caninum_9.3.2.ec.cg.pg (net) Ancylostoma_duodenale - Ancylostoma duodenale The Genome Institute Jan. 2015 - GCA_000816745.1 - A_duodenale_2.2.ec.cg.pg (net) Angiostrongylus_cantonensis - Angiostrongylus cantonensis University of Malaya Nov. 2016 - GCA_001884285.1 - ASM188428v1 (net) Ascaris_suum - Ascaris suum Genetics and Genome Center, Washington University School of Medicine Nov. 2017 - GCA_000187025.3 - ASM18702v3 (net) Barber pole worm - Haemonchus contortus Jul. 2013 (WormBase WS239/haeCon2) (net) Brugia_malayi - Brugia malayi TIGR Mar. 2008 - GCF_000002995.3 - ASM299v2 (net) Brugia_pahangi - Brugia pahangi University Malaya Sep. 2015 - GCA_001280985.1 - Brugia_pa_1.0 (net) Bursaphelenchus_xylophilus - Bursaphelenchus xylophilus Wellcome Trust Sanger insititute Oct. 2011 - GCA_000231135.1 - ASM23113v1 (net) C. angaria - Caenorhabditis angaria Apr. 2012 (WS232/ps1010rel8/caeAng2) (net) C. brenneri - Caenorhabditis brenneri Nov. 2010 (C. brenneri 6.0.1b/caePb3) (net) C. briggsae - Caenorhabditis briggsae Apr. 2011 (WS225/cb4) (net) C. intestinalis - Ciona intestinalis Apr. 2011 (Kyoto KH/ci3) (net) C. japonica - Caenorhabditis japonica Aug. 2010 (WUSTL 7.0.1/caeJap4) (net) C. remanei - Caenorhabditis remanei Jul. 2007 (WS220/caeRem4) (net) C. sp. 5 ju800 - Caenorhabditis sp5 ju800 Jan. 2012 (WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51) (net) C. tropicalis - Caenorhabditis tropicalis Nov. 2010 (WS226/WUSTL 3.0.1/caeSp111) (net) C_briggsae - Caenorhabditis briggsae The C.briggsae Sequencing Consortium Jul. 2014 - GCA_000004555.3 - CB4 (net) C_latens - Caenorhabditis latens University of Oregon Aug. 2017 - GCA_002259235.1 - CaeLat1.0 (net) C_nigoni - Caenorhabditis nigoni Cornell University Nov. 2017 - GCA_002742825.1 - nigoni.pc_2016.07.14 (net) C_sp21_LS_2015 - Caenorhabditis sp. 21 LS-2015 BANG Aug. 2018 - GCA_900536235.1 - CPARV_v1 (net) C_sp26_LS_2015 - Caenorhabditis sp. 26 LS-2015 BANG Aug. 2018 - GCA_900536285.1 - CZANZ_v1 (net) C_sp31_LS_2015 - Caenorhabditis sp. 31 LS-2015 BANG Aug. 2018 - GCA_900536295.1 - CUTEL_v1 (net) C_sp32_LS_2015 - Caenorhabditis sp. 32 LS-2015 BANG Aug. 2018 - GCA_900536325.1 - CSULS_v1 (net) C_sp34_TK_2017 - Caenorhabditis sp. 34 TK-2017 University of Miyazaki Jun. 2017 - GCA_003052745.1 - Sp34_v7 (net) C_sp38_MB_2015 - Caenorhabditis sp. 38 MB-2015 BANG Aug. 2018 - GCA_900536415.1 - CQUIO_v1 (net) C_sp39_LS_2015 - Caenorhabditis sp. 39 LS-2015 BANG Aug. 2018 - GCA_900536345.1 - CWAIT_v1 (net) C_sp40_LS_2015 - Caenorhabditis sp. 40 LS-2015 BANG Aug. 2018 - GCA_900536305.1 - CTRIB_v1 (net) Clonorchis_sinensis - Clonorchis sinensis Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University Nov. 2011 - GCA_000236345.1 - C_sinensis-2.0 (net) Dicrocoelium_dendriticum - Dicrocoelium dendriticum WTSI Sep. 2014 - GCA_000950715.1 - D_dendriticum_Leon_v1_0_4 (net) Dictyocaulus_viviparus - Dictyocaulus viviparus The Genome Institute Mar. 2015 - GCA_000816705.1 - D_viviparus_9.2.1.ec.pg (net) Diploscapter_coronatus - Diploscapter coronatus NIG Jun. 2017 - GCA_002207785.1 - ASM220778v1 (net) Diploscapter_pachys - Diploscapter pachys New York University Sep. 2017 - GCA_002287525.1 - DipSp1Ass11Ann3 (net) Dirofilaria_immitis - Dirofilaria immitis EDINBURGH Aug. 2013 - GCA_001077395.1 - ASM107739v1 (net) Ditylenchus_destructor - Ditylenchus destructor Huazhong Agricultural University Mar. 2016 - GCA_001579705.1 - ASM157970v1 (net) Dog heartworm - Dirofilaria immitis Sep. 2013 (WS240/D. immitis v2.2/dirImm1) (net) Dugesia_japonica - Dugesia japonica University of Oxford Jan. 2017 - GCA_001938525.1 - Djap_assembly_v1 (net) Echinococcus_canadensis - Echinococcus canadensis IMPAM-UBA-CONICET May 2016 - GCA_900004735.1 - ECANG7 (net) Echinococcus_granulosus - Echinococcus granulosus Chinese National Human Genome Center at Shanghai Jan. 2014 - GCA_000524195.1 - ASM52419v1 (net) Echinococcus_multilocularis - Echinococcus multilocularis WTSI Dec. 2015 - GCA_000469725.3 - EMULTI002 (net) Elaeophora_elaphi - Elaeophora elaphi SC Nov. 2013 - GCA_000499685.1 - EEL001 (net) Eye worm - Loa loa Jul. 2012 (WS235/L_loa_Cameroon_isolate/loaLoa1) (net) Fasciola_gigantica - Fasciola gigantica North-Eastern Hill University Jan. 2018 - GCA_002867515.1 - ASM286751v1 (net) Fasciola_hepatica - Fasciola hepatica LIV Apr. 2018 - GCA_900302435.1 - Fasciola_10x_pilon (net) Filarial worm - Brugia malayi May. 2014 (WS244/B_malayi-3.1/bruMal2) (net) Girardia_tigrina - Girardia tigrina University of Oxford Jan. 2017 - GCA_001938485.1 - gtig.1 (net) Globodera_ellingtonae - Globodera ellingtonae Oregon State University Sep. 2016 - GCA_001723225.1 - ASM172322v1 (net) Globodera_pallida - Globodera pallida WTSI May 2014 - GCA_000724045.1 - GPAL001 (net) Globodera_rostochiensis - Globodera rostochiensis BANG Apr. 2016 - GCA_900079975.1 - nGr (net) Gyrodactylus_salaris - Gyrodactylus salaris Natural History Museum, University of Oslo Jun. 2014 - GCA_000715275.1 - Gsalaris_v1 (net) H. bacteriophora/m31e - Heterorhabditis bacteriophora Aug. 2011 (WS229/H. bacteriophora 7.0/hetBac1) (net) Haemonchus_contortus - Haemonchus contortus SC Aug. 2013 - GCA_000469685.1 - HCON (net) Heligmosomoides_polygyrus_bakeri - Heligmosomoides polygyrus bakeri BANG Sep. 2016 - GCA_900096555.1 - nHp_v2.0 (net) Heterodera_glycines - Heterodera glycines Monsanto Apr. 2008 - GCA_000150805.1 - HG2 (net) Hymenolepis_microstoma - Hymenolepis microstoma WTSI Dec. 2015 - GCA_000469805.2 - HMIC002 (net) Loa_loa - Loa loa Broad Institute Jul. 2012 - GCF_000183805.2 - Loa_loa_V3.1 (net) M. hapla - Meloidogyne hapla Sep. 2008 (M. hapla VW9 WS210/melHap1) (net) M. incognita - Meloidogyne incognita Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2) (net) Macrostomum_lignano - Macrostomum lignano University Medical Center Groningen Aug. 2017 - GCA_002269645.1 - Mlig_3_7 (net) Meloidogyne_arenaria - Meloidogyne arenaria RIKEN May 2018 - GCA_003133805.1 - ASM313380v1 (net) Meloidogyne_floridensis - Meloidogyne floridensis BANG Jun. 2014 - GCA_000751915.1 - nMf_1_1 (net) Meloidogyne_graminicola - Meloidogyne graminicola ICAR-IARI, New Delhi, INDIA Nov. 2017 - GCA_002778205.1 - Mgraminicola_V1 (net) Meloidogyne_incognita - Meloidogyne incognita Genoscope CEA May 2017 - GCA_900182535.1 - Meloidogyne_incognita_V3 (net) Meloidogyne_javanica - Meloidogyne javanica Genoscope CEA Apr. 2017 - GCA_900003945.1 - ASM90000394v1 (net) Microworm - Panagrellus redivivus Feb. 2013 (WS240/Pred3/panRed1) (net) N. americanus - Necator americanus Dec. 2013 (WS242/N_americanus_v1/necAme1) (net) Necator_americanus - Necator americanus The Genome Institute at Washington University Dec. 2013 - GCF_000507365.1 - N_americanus_v1 (net) Nippostrongylus_brasiliensis - Nippostrongylus brasiliensis Malaghan Institute of Medical Research Aug. 2017 - GCA_900200055.1 - NbL5_MIMR_Canu1.5 (net) O. volvulus - Onchocerca volvulus Nov. 2013 (WS241/O_volvulus_Cameroon_v3/oncVol1) (net) Oesophagostomum_dentatum - Oesophagostomum dentatum The Genome Institute Dec. 2014 - GCA_000797555.1 - O_dentatum_10.0.ec.cg.pg (net) Onchocerca_flexuosa - Onchocerca flexuosa The Genome Institute Aug. 2017 - GCA_002249935.1 - O_flexuosa_1.0.allpaths.pg.lrna (net) Onchocerca_ochengi - Onchocerca ochengi WTSI Mar. 2016 - GCA_000950515.2 - O_ochengi_Ngaoundere (net) Onchocerca_volvulus - Onchocerca volvulus SC Feb. 2014 - GCA_000499405.2 - ASM49940v2 (net) Opisthorchis_viverrini - Opisthorchis viverrini The University of Melbourne Jul. 2014 - GCA_000715545.1 - OpiViv1.0 (net) Oscheius_MCB - Oscheius sp. MCB University of the Witwatersrand Feb. 2015 - GCA_000934875.1 - ASM93487v1 (net) Oscheius_TEL_2014 - Oscheius sp. TEL-2014 University of the Witwatersrand Jan. 2016 - GCA_001513535.1 - ASM151353v1 (net) Oscheius_tipulae - Oscheius tipulae BANG May 2017 - GCA_900184235.1 - Oscheius_tipulae_assembly_v2 (net) P. exspectatus - Pristionchus exspectatus Mar. 2014 (WS243/P_exspectatus_v1/priExs1) (net) P. pacificus - Pristionchus pacificus Aug. 2014 (WS221/P_pacificus-v2/priPac3) (net) Parapristionchus_giblindavisi - Parapristionchus giblindavisi MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY Jun. 2018 - GCA_900491355.1 - Parapristionchus_genome (net) Parascaris_univalens - Parascaris univalens University of Colorado School of Medicine Aug. 2017 - GCA_002259215.1 - ASM225921v1 (net) Parastrongyloides_trichosuri - Parastrongyloides trichosuri SC Sep. 2014 - GCA_000941615.1 - P_trichosuri_KNP (net) Pig roundworm - Ascaris suum Sep. 2012 (WS229/AscSuum_1.0/ascSuu1) (net) Pine wood nematode - Bursaphelenchus xylophilus Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1) (net) Plectus_sambesii - Plectus sambesii MRC London Institute of Medical Sciences - Imperial College London Nov. 2017 - GCA_002796945.1 - Psam_v1.0 (net) Pristionchus_arcanus - Pristionchus arcanus MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY Jun. 2018 - GCA_900490705.1 - P._arcanus_genome (net) Pristionchus_entomophagus - Pristionchus entomophagus MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY Jun. 2018 - GCA_900490825.1 - P._entomophagus_genome (net) Pristionchus_exspectatus - Pristionchus exspectatus MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY May 2018 - GCA_900380275.1 - Pristionchus_exspectatus_de_novo_assembly (net) Pristionchus_maxplancki - Pristionchus maxplancki MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY Jun. 2018 - GCA_900490775.1 - Prisstionchus_maxplancki_genome (net) Pristionchus_pacificus - Pristionchus pacificus Washington University (WashU) Oct. 2017 - GCA_000180635.3 - El_Paco (net) Rhabditophanes_KR3021 - Rhabditophanes sp. KR3021 WTSI Sep. 2014 - GCA_000944355.1 - Rhabditophanes_sp_KR3021 (net) Romanomermis_culicivorax - Romanomermis culicivorax UZK Jan. 2014 - GCA_001039655.1 - nRc.2.0 (net) Rotylenchulus_reniformis - Rotylenchulus reniformis Mississippi State University Jun. 2015 - GCA_001026735.1 - RREN1.0 (net) Schistosoma_haematobium - Schistosoma haematobium The University of Melbourne Jun. 2014 - GCA_000699445.1 - SchHae_1.0 (net) Schistosoma_japonicum - Schistosoma japonicum Chinese Human Genome Center at Shanghai Apr. 2009 - GCA_000151775.1 - ASM15177v1 (net) Schistosoma_mansoni - Schistosoma mansoni Schistosoma Genome Network Dec. 2011 - GCA_000237925.2 - ASM23792v2 (net) Schmidtea_mediterranea - Schmidtea mediterranea Max Planck Institute of Molecular Cell Biology and Genetics Oct. 2017 - GCA_002600895.1 - ASM260089v1 (net) Setaria_digitata - Setaria digitata SVERIGES LANTBRUKSUNIVERSITET Jan. 2018 - GCA_900083525.1 - Sdigitata (net) Setaria_equina - Setaria equina Beni-Suef University Mar. 2018 - GCA_003012265.1 - Setequ3.0 (net) Spirometra_erinaceieuropaei - Spirometra erinaceieuropaei WTSI Sep. 2014 - GCA_000951995.1 - S_erinaceieuropaei (net) Steinernema_carpocapsae - Steinernema carpocapsae California Institute of Technology Sep. 2014 - GCA_000757645.1 - S_carpo_v1 (net) Steinernema_feltiae - Steinernema feltiae California Institute of Technology Sep. 2014 - GCA_000757705.1 - S_felt_v1 (net) Steinernema_glaseri - Steinernema glaseri California Institute of Technology Sep. 2014 - GCA_000757755.1 - S_glas_v1 (net) Steinernema_monticolum - Steinernema monticolum California Institute of Technology Dec. 2013 - GCA_000505645.1 - S_monti_v1 (net) Steinernema_scapterisci - Steinernema scapterisci California Institute of Technology Sep. 2014 - GCA_000757745.1 - S_scapt_v1 (net) Strongyloides_papillosus - Strongyloides papillosus SC Nov. 2014 - GCA_000936265.1 - S_papillosus_LIN (net) Strongyloides_stercoralis - Strongyloides stercoralis SC Nov. 2014 - GCA_000947215.1 - S_stercoralis_PV0001 (net) Strongyloides_venezuelensis - Strongyloides venezuelensis SC Jun. 2015 - GCA_001028725.1 - S_venezuelensis_HH1 (net) Subanguina_moxae - Subanguina moxae Faculty of medicine, University of Miyazaki Apr. 2015 - GCA_000981365.1 - SAMX_assembly_v0.8 (net) Taenia_asiatica - Taenia asiatica Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences Sep. 2016 - GCA_001693035.2 - Taenia_asiatica_TASYD01_v1 (net) Taenia_multiceps - Taenia multiceps Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Jul. 2018 - GCA_001923025.2 - T_multiceps_v2.0 (net) Taenia_saginata - Taenia saginata Beijing Institute of Genomics, Chinese Academy of Science Oct. 2016 - GCA_001693075.2 - ASM169307v2 (net) Taenia_solium - Taenia solium Taenia solium Genome Consortium Nov. 2016 - GCA_001870725.1 - MEX_genome_complete.1-6-13 (net) Teladorsagia_circumcincta - Teladorsagia circumcincta The Genome Institute Sep. 2017 - GCA_002352805.1 - T_circumcincta.14.0.ec.cg.pg (net) Threadworm - Strongyloides ratti Sep. 2014 (S. ratti ED321/strRat2) (net) Toxocara_canis - Toxocara canis University of Melbourne Dec. 2014 - GCA_000803305.1 - Toxocara_canis_adult_r1.0 (net) Trichinella - Trichinella spiralis Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1) (net) Trichinella_T6 - Trichinella sp. T6 University of Melbourne Nov. 2015 - GCA_001447435.1 - T6_ISS34_r1.0 (net) Trichinella_T8 - Trichinella sp. T8 University of Melbourne Nov. 2015 - GCA_001447745.1 - T8_ISS272_r1.0 (net) Trichinella_T9 - Trichinella sp. T9 University of Melbourne Nov. 2015 - GCA_001447505.1 - T9_ISS409_r1.0 (net) Trichinella_britovi - Trichinella britovi University of Melbourne Nov. 2015 - GCA_001447585.1 - T3_ISS120_r1.0 (net) Trichinella_murrelli - Trichinella murrelli USDA-ARS Jul. 2017 - GCA_002221485.1 - ASM222148v1 (net) Trichinella_nativa - Trichinella nativa University of Melbourne Nov. 2015 - GCA_001447565.1 - T2_ISS10_r1.0 (net) Trichinella_nelsoni - Trichinella nelsoni University of Melbourne Nov. 2015 - GCA_001447455.1 - T7_ISS37_r1.0 (net) Trichinella_papuae - Trichinella papuae University of Melbourne Nov. 2015 - GCA_001447755.1 - T10_ISS1980_r1.0 (net) Trichinella_patagoniensis - Trichinella patagoniensis University of Melbourne Nov. 2015 - GCA_001447655.1 - T12_ISS2496_r1.0 (net) Trichinella_pseudospiralis - Trichinella pseudospiralis University of Melbourne Nov. 2015 - GCA_001447725.1 - T4_ISS588_r1.0 (net) Trichinella_spiralis - Trichinella spiralis Washington University School of Medicine Jan. 2011 - GCF_000181795.1 - Trichinella_spiralis-3.7.1 (net) Trichinella_zimbabwensis - Trichinella zimbabwensis University of Melbourne Nov. 2015 - GCA_001447665.1 - T11_ISS1029_r1.0 (net) Trichuris_muris - Trichuris muris WTSI Mar. 2014 - GCA_000612645.1 - TMUE2.2 (net) Trichuris_trichiura - Trichuris trichiura SC Mar. 2014 - GCA_000613005.1 - TTRE2.1 (net) Whipworm - Trichuris suis Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1) (net) Wuchereria_bancrofti - Wuchereria bancrofti Case Western Reserve University Feb. 2016 - GCA_001555675.1 - Wb_PNG_Genome_assembly_pt22 (net) --------------------------------------------------------------- To download a large file or multiple files from this directory, we recommend that you use rsync or ftp rather than downloading the files via our website. There is approximately 14 Gb of compressed data in this directory, approximately 100 Gb uncompressed. Via rsync: rsync -av --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/ce11/multiz135way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: go to the directory goldenPath/ce11/multiz135way To download multiple files from the UNIX command line, use the "mget" command. mget ... - or - mget -a (to download all the files in the directory) Use the "prompt" command to toggle the interactive mode if you do not want to be prompted for each file that you download. --------------------------------------------------------------- All the files in this directory are freely usable for any purpose. For data use restrictions regarding the individual genome assemblies, see http://genome.ucsc.edu/goldenPath/credits.html.