This file is from: http://hgdownload.cse.ucsc.edu/goldenPath/ce11/phyloP135way/README.txt This directory contains conversation scoring by phyloP (phylogenetic p-values) from the PHAST package (http://compgen.bscb.cornell.edu/phast/) for multiple alignments of 134 genomes to the C. elegans genome: 111 nematodes, 22 flatworms and one Ciona intestinalis. Files in this directory are: ce11.phyloP135way.mod phyloP tree model with branch lengths for all the sequences *** 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. chr*.phyloP135way.wigFix.gz - phyloP scores for all the alignments in fixed step wiggle format ce11.phyloP135way.bw - phyloP scores for all the alignments in bigWig format md5sum.txt - md5 sums of the files here to verify accurate download The multiple alignments and methods description are at: http://hgdownload.cse.ucsc.edu/goldenPath/ce11/multiz135way/ For more information about this data, see the track description for the Conservation track: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=ce11&g=cons135way For a description of the phyloP wigFix data file format, see: http://genome.ucsc.edu/goldenPath/help/phastCons.html see also the section describing the 'fixedStep' wiggle format: http://genome.ucsc.edu/goldenPath/help/wiggle.html 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 535 Mb of compressed data in this directory, approximately 920 Mb uncompressed.. Via rsync: rsync -avz --progress \ rsync://hgdownload.cse.ucsc.edu/goldenPath/ce11/phyloP135way/ ./ Via FTP: ftp hgdownload.cse.ucsc.edu user name: anonymous password: <your email address> go to the directory goldenPath/ce11/phyloP135way To download multiple files from the UNIX command line, use the "mget" command. mget <filename1> <filename2> ... - 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 available for public use. For data use restrictions regarding the genome assemblies used in this annotation, see http://genome.ucsc.edu/goldenPath/credits.html. --------------------------------------------------------------- References for phastCons and phyloP: Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. (http://genome.cshlp.org/content/20/1/110.long) Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. (http://genome.cshlp.org/content/15/8/1034.full) ---------------------------------------------------------------
Name Last modified Size Description
Parent Directory - md5sum.txt 2018-12-17 14:57 549 ce11.phyloP135way.bw 2018-12-14 17:17 340M chrX.phyloP135way.wigFix.gz 2018-12-14 17:16 35M chrV.phyloP135way.wigFix.gz 2018-12-14 17:16 41M chrM.phyloP135way.wigFix.gz 2018-12-14 17:16 33K chrIV.phyloP135way.wigFix.gz 2018-12-14 17:16 35M chrIII.phyloP135way.wigFix.gz 2018-12-14 17:15 27M chrII.phyloP135way.wigFix.gz 2018-12-14 17:15 29M chrI.phyloP135way.wigFix.gz 2018-12-14 17:15 29M ce11.phyloP135way.mod 2018-12-14 14:59 5.4K