This track shows multiple alignments of 135 species: 112 nematodes, 22 flatworms and one Ciona intestinalis sequence and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 135 species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.
The 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. See also: Phylip distance operations, assembly and alignment-free phylogeny reconstruction, and recapitulating phylogenies using k-mers.
PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).
Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1.
Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data.
See also: lastz parameters and other details, and chain minimum score and gap parameters used in these alignments.
Missing sequence in the assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see Gap Annotation, below).
Downloads for data in this track are available:
Organism Species Assembly name browser or
NCBI sourcealignment type C. elegans Caenorhabditis elegans Feb. 2013 (WBcel235/ce11) Feb. 2013 (WBcel235/ce11) reference A. ceylanicum Ancylostoma ceylanicum Mar. 2014 (WS243/Acey_2013.11.30.genDNA/ancCey1) Mar. 2014 (WS243/Acey_2013.11.30.genDNA/ancCey1) net Acrobeloides_nanus Acrobeloides nanus Jun. 2018 (v1) GCA_900406225.1 net Ancylostoma_caninum Ancylostoma caninum Jul. 2018 (A_caninum_9.3.2.ec.cg.pg) GCA_003336725.1 net Ancylostoma_duodenale Ancylostoma duodenale Jan. 2015 (A_duodenale_2.2.ec.cg.pg) GCA_000816745.1 net Angiostrongylus_cantonensis Angiostrongylus cantonensis Nov. 2016 (ASM188428v1) GCA_001884285.1 net Ascaris_suum Ascaris suum Nov. 2017 (ASM18702v3) GCA_000187025.3 net Barber pole worm Haemonchus contortus Jul. 2013 (WormBase WS239/haeCon2) Jul. 2013 (WormBase WS239/haeCon2) net Brugia_malayi Brugia malayi Mar. 2008 (ASM299v2) GCF_000002995.3 net Brugia_pahangi Brugia pahangi Sep. 2015 (Brugia_pa_1.0) GCA_001280985.1 net Bursaphelenchus_xylophilus Bursaphelenchus xylophilus Oct. 2011 (ASM23113v1) GCA_000231135.1 net C. angaria Caenorhabditis angaria Apr. 2012 (WS232/ps1010rel8/caeAng2) Apr. 2012 (WS232/ps1010rel8/caeAng2) net C. brenneri Caenorhabditis brenneri Nov. 2010 (C. brenneri 6.0.1b/caePb3) Nov. 2010 (C. brenneri 6.0.1b/caePb3) net C. briggsae Caenorhabditis briggsae Apr. 2011 (WS225/cb4) Apr. 2011 (WS225/cb4) net C. intestinalis Ciona intestinalis Apr. 2011 (Kyoto KH/ci3) Apr. 2011 (Kyoto KH/ci3) net C. japonica Caenorhabditis japonica Aug. 2010 (WUSTL 7.0.1/caeJap4) Aug. 2010 (WUSTL 7.0.1/caeJap4) net C. remanei Caenorhabditis remanei Jul. 2007 (WS220/caeRem4) Jul. 2007 (WS220/caeRem4) net C. sp. 5 ju800 Caenorhabditis sp5 ju800 Jan. 2012 (WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51) Jan. 2012 (WS230/Caenorhabditis_sp_5-JU800-1.0/caeSp51) net C. tropicalis Caenorhabditis tropicalis Nov. 2010 (WS226/WUSTL 3.0.1/caeSp111) Nov. 2010 (WS226/WUSTL 3.0.1/caeSp111) net C_briggsae Caenorhabditis briggsae Jul. 2014 (CB4) GCA_000004555.3 net C_latens Caenorhabditis latens Aug. 2017 (CaeLat1.0) GCA_002259235.1 net C_nigoni Caenorhabditis nigoni Nov. 2017 (nigoni.pc_2016.07.14) GCA_002742825.1 net C_sp21_LS_2015 Caenorhabditis sp. 21 LS-2015 Aug. 2018 (CPARV_v1) GCA_900536235.1 net C_sp26_LS_2015 Caenorhabditis sp. 26 LS-2015 Aug. 2018 (CZANZ_v1) GCA_900536285.1 net C_sp31_LS_2015 Caenorhabditis sp. 31 LS-2015 Aug. 2018 (CUTEL_v1) GCA_900536295.1 net C_sp32_LS_2015 Caenorhabditis sp. 32 LS-2015 Aug. 2018 (CSULS_v1) GCA_900536325.1 net C_sp34_TK_2017 Caenorhabditis sp. 34 TK-2017 Jun. 2017 (Sp34_v7) GCA_003052745.1 net C_sp38_MB_2015 Caenorhabditis sp. 38 MB-2015 Aug. 2018 (CQUIO_v1) GCA_900536415.1 net C_sp39_LS_2015 Caenorhabditis sp. 39 LS-2015 Aug. 2018 (CWAIT_v1) GCA_900536345.1 net C_sp40_LS_2015 Caenorhabditis sp. 40 LS-2015 Aug. 2018 (CTRIB_v1) GCA_900536305.1 net Clonorchis_sinensis Clonorchis sinensis Nov. 2011 (C_sinensis-2.0) GCA_000236345.1 net Dicrocoelium_dendriticum Dicrocoelium dendriticum Sep. 2014 (D_dendriticum_Leon_v1_0_4) GCA_000950715.1 net Dictyocaulus_viviparus Dictyocaulus viviparus Mar. 2015 (D_viviparus_9.2.1.ec.pg) GCA_000816705.1 net Diploscapter_coronatus Diploscapter coronatus Jun. 2017 (ASM220778v1) GCA_002207785.1 net Diploscapter_pachys Diploscapter pachys Sep. 2017 (DipSp1Ass11Ann3) GCA_002287525.1 net Dirofilaria_immitis Dirofilaria immitis Aug. 2013 (ASM107739v1) GCA_001077395.1 net Ditylenchus_destructor Ditylenchus destructor Mar. 2016 (ASM157970v1) GCA_001579705.1 net Dog heartworm Dirofilaria immitis Sep. 2013 (WS240/D. immitis v2.2/dirImm1) Sep. 2013 (WS240/D. immitis v2.2/dirImm1) net Dugesia_japonica Dugesia japonica Jan. 2017 (Djap_assembly_v1) GCA_001938525.1 net Echinococcus_canadensis Echinococcus canadensis May 2016 (ECANG7) GCA_900004735.1 net Echinococcus_granulosus Echinococcus granulosus Jan. 2014 (ASM52419v1) GCA_000524195.1 net Echinococcus_multilocularis Echinococcus multilocularis Dec. 2015 (EMULTI002) GCA_000469725.3 net Elaeophora_elaphi Elaeophora elaphi Nov. 2013 (EEL001) GCA_000499685.1 net Eye worm Loa loa Jul. 2012 (WS235/L_loa_Cameroon_isolate/loaLoa1) Jul. 2012 (WS235/L_loa_Cameroon_isolate/loaLoa1) net Fasciola_gigantica Fasciola gigantica Jan. 2018 (ASM286751v1) GCA_002867515.1 net Fasciola_hepatica Fasciola hepatica Apr. 2018 (Fasciola_10x_pilon) GCA_900302435.1 net Filarial worm Brugia malayi May. 2014 (WS244/B_malayi-3.1/bruMal2) May. 2014 (WS244/B_malayi-3.1/bruMal2) net Girardia_tigrina Girardia tigrina Jan. 2017 (gtig.1) GCA_001938485.1 net Globodera_ellingtonae Globodera ellingtonae Sep. 2016 (ASM172322v1) GCA_001723225.1 net Globodera_pallida Globodera pallida May 2014 (GPAL001) GCA_000724045.1 net Globodera_rostochiensis Globodera rostochiensis Apr. 2016 (nGr) GCA_900079975.1 net Gyrodactylus_salaris Gyrodactylus salaris Jun. 2014 (Gsalaris_v1) GCA_000715275.1 net H. bacteriophora/m31e Heterorhabditis bacteriophora Aug. 2011 (WS229/H. bacteriophora 7.0/hetBac1) Aug. 2011 (WS229/H. bacteriophora 7.0/hetBac1) net Haemonchus_contortus Haemonchus contortus Aug. 2013 (HCON) GCA_000469685.1 net Heligmosomoides_polygyrus_bakeri Heligmosomoides polygyrus bakeri Sep. 2016 (nHp_v2.0) GCA_900096555.1 net Heterodera_glycines Heterodera glycines Apr. 2008 (HG2) GCA_000150805.1 net Hymenolepis_microstoma Hymenolepis microstoma Dec. 2015 (HMIC002) GCA_000469805.2 net Loa_loa Loa loa Jul. 2012 (Loa_loa_V3.1) GCF_000183805.2 net M. hapla Meloidogyne hapla Sep. 2008 (M. hapla VW9 WS210/melHap1) Sep. 2008 (M. hapla VW9 WS210/melHap1) net M. incognita Meloidogyne incognita Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2) Feb. 2008 (M. incognita WS245/PRJEA28837/melInc2) net Macrostomum_lignano Macrostomum lignano Aug. 2017 (Mlig_3_7) GCA_002269645.1 net Meloidogyne_arenaria Meloidogyne arenaria May 2018 (ASM313380v1) GCA_003133805.1 net Meloidogyne_floridensis Meloidogyne floridensis Jun. 2014 (nMf_1_1) GCA_000751915.1 net Meloidogyne_graminicola Meloidogyne graminicola Nov. 2017 (Mgraminicola_V1) GCA_002778205.1 net Meloidogyne_incognita Meloidogyne incognita May 2017 (Meloidogyne_incognita_V3) GCA_900182535.1 net Meloidogyne_javanica Meloidogyne javanica Apr. 2017 (ASM90000394v1) GCA_900003945.1 net Microworm Panagrellus redivivus Feb. 2013 (WS240/Pred3/panRed1) Feb. 2013 (WS240/Pred3/panRed1) net N. americanus Necator americanus Dec. 2013 (WS242/N_americanus_v1/necAme1) Dec. 2013 (WS242/N_americanus_v1/necAme1) net Necator_americanus Necator americanus Dec. 2013 (N_americanus_v1) GCF_000507365.1 net Nippostrongylus_brasiliensis Nippostrongylus brasiliensis Aug. 2017 (NbL5_MIMR_Canu1.5) GCA_900200055.1 net O. volvulus Onchocerca volvulus Nov. 2013 (WS241/O_volvulus_Cameroon_v3/oncVol1) Nov. 2013 (WS241/O_volvulus_Cameroon_v3/oncVol1) net Oesophagostomum_dentatum Oesophagostomum dentatum Dec. 2014 (O_dentatum_10.0.ec.cg.pg) GCA_000797555.1 net Onchocerca_flexuosa Onchocerca flexuosa Aug. 2017 (O_flexuosa_1.0.allpaths.pg.lrna) GCA_002249935.1 net Onchocerca_ochengi Onchocerca ochengi Mar. 2016 (O_ochengi_Ngaoundere) GCA_000950515.2 net Onchocerca_volvulus Onchocerca volvulus Feb. 2014 (ASM49940v2) GCA_000499405.2 net Opisthorchis_viverrini Opisthorchis viverrini Jul. 2014 (OpiViv1.0) GCA_000715545.1 net Oscheius_MCB Oscheius sp. MCB Feb. 2015 (ASM93487v1) GCA_000934875.1 net Oscheius_TEL_2014 Oscheius sp. TEL-2014 Jan. 2016 (ASM151353v1) GCA_001513535.1 net Oscheius_tipulae Oscheius tipulae May 2017 (Oscheius_tipulae_assembly_v2) GCA_900184235.1 net P. exspectatus Pristionchus exspectatus Mar. 2014 (WS243/P_exspectatus_v1/priExs1) Mar. 2014 (WS243/P_exspectatus_v1/priExs1) net P. pacificus Pristionchus pacificus Aug. 2014 (WS221/P_pacificus-v2/priPac3) Aug. 2014 (WS221/P_pacificus-v2/priPac3) net Parapristionchus_giblindavisi Parapristionchus giblindavisi Jun. 2018 (Parapristionchus_genome) GCA_900491355.1 net Parascaris_univalens Parascaris univalens Aug. 2017 (ASM225921v1) GCA_002259215.1 net Parastrongyloides_trichosuri Parastrongyloides trichosuri Sep. 2014 (P_trichosuri_KNP) GCA_000941615.1 net Pig roundworm Ascaris suum Sep. 2012 (WS229/AscSuum_1.0/ascSuu1) Sep. 2012 (WS229/AscSuum_1.0/ascSuu1) net Pine wood nematode Bursaphelenchus xylophilus Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1) Nov. 2011 (WS229/B. xylophilus Ka4C1/burXyl1) net Plectus_sambesii Plectus sambesii Nov. 2017 (Psam_v1.0) GCA_002796945.1 net Pristionchus_arcanus Pristionchus arcanus Jun. 2018 (P._arcanus_genome) GCA_900490705.1 net Pristionchus_entomophagus Pristionchus entomophagus Jun. 2018 (P._entomophagus_genome) GCA_900490825.1 net Pristionchus_exspectatus Pristionchus exspectatus May 2018 (Pristionchus_exspectatus_de_novo_assembly) GCA_900380275.1 net Pristionchus_maxplancki Pristionchus maxplancki Jun. 2018 (Prisstionchus_maxplancki_genome) GCA_900490775.1 net Pristionchus_pacificus Pristionchus pacificus Oct. 2017 (El_Paco) GCA_000180635.3 net Rhabditophanes_KR3021 Rhabditophanes sp. KR3021 Sep. 2014 (Rhabditophanes_sp_KR3021) GCA_000944355.1 net Romanomermis_culicivorax Romanomermis culicivorax Jan. 2014 (nRc.2.0) GCA_001039655.1 net Rotylenchulus_reniformis Rotylenchulus reniformis Jun. 2015 (RREN1.0) GCA_001026735.1 net Schistosoma_haematobium Schistosoma haematobium Jun. 2014 (SchHae_1.0) GCA_000699445.1 net Schistosoma_japonicum Schistosoma japonicum Apr. 2009 (ASM15177v1) GCA_000151775.1 net Schistosoma_mansoni Schistosoma mansoni Dec. 2011 (ASM23792v2) GCA_000237925.2 net Schmidtea_mediterranea Schmidtea mediterranea Oct. 2017 (ASM260089v1) GCA_002600895.1 net Setaria_digitata Setaria digitata Jan. 2018 (Sdigitata) GCA_900083525.1 net Setaria_equina Setaria equina Mar. 2018 (Setequ3.0) GCA_003012265.1 net Spirometra_erinaceieuropaei Spirometra erinaceieuropaei Sep. 2014 (S_erinaceieuropaei) GCA_000951995.1 net Steinernema_carpocapsae Steinernema carpocapsae Sep. 2014 (S_carpo_v1) GCA_000757645.1 net Steinernema_feltiae Steinernema feltiae Sep. 2014 (S_felt_v1) GCA_000757705.1 net Steinernema_glaseri Steinernema glaseri Sep. 2014 (S_glas_v1) GCA_000757755.1 net Steinernema_monticolum Steinernema monticolum Dec. 2013 (S_monti_v1) GCA_000505645.1 net Steinernema_scapterisci Steinernema scapterisci Sep. 2014 (S_scapt_v1) GCA_000757745.1 net Strongyloides_papillosus Strongyloides papillosus Nov. 2014 (S_papillosus_LIN) GCA_000936265.1 net Strongyloides_stercoralis Strongyloides stercoralis Nov. 2014 (S_stercoralis_PV0001) GCA_000947215.1 net Strongyloides_venezuelensis Strongyloides venezuelensis Jun. 2015 (S_venezuelensis_HH1) GCA_001028725.1 net Subanguina_moxae Subanguina moxae Apr. 2015 (SAMX_assembly_v0.8) GCA_000981365.1 net Taenia_asiatica Taenia asiatica Sep. 2016 (Taenia_asiatica_TASYD01_v1) GCA_001693035.2 net Taenia_multiceps Taenia multiceps Jul. 2018 (T_multiceps_v2.0) GCA_001923025.2 net Taenia_saginata Taenia saginata Oct. 2016 (ASM169307v2) GCA_001693075.2 net Taenia_solium Taenia solium Nov. 2016 (MEX_genome_complete.1-6-13) GCA_001870725.1 net Teladorsagia_circumcincta Teladorsagia circumcincta Sep. 2017 (T_circumcincta.14.0.ec.cg.pg) GCA_002352805.1 net Threadworm Strongyloides ratti Sep. 2014 (S. ratti ED321/strRat2) Sep. 2014 (S. ratti ED321/strRat2) net Toxocara_canis Toxocara canis Dec. 2014 (Toxocara_canis_adult_r1.0) GCA_000803305.1 net Trichinella Trichinella spiralis Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1) Jan. 2011 (WS225/Trichinella_spiralis-3.7.1/triSpi1) net Trichinella_T6 Trichinella sp. T6 Nov. 2015 (T6_ISS34_r1.0) GCA_001447435.1 net Trichinella_T8 Trichinella sp. T8 Nov. 2015 (T8_ISS272_r1.0) GCA_001447745.1 net Trichinella_T9 Trichinella sp. T9 Nov. 2015 (T9_ISS409_r1.0) GCA_001447505.1 net Trichinella_britovi Trichinella britovi Nov. 2015 (T3_ISS120_r1.0) GCA_001447585.1 net Trichinella_murrelli Trichinella murrelli Jul. 2017 (ASM222148v1) GCA_002221485.1 net Trichinella_nativa Trichinella nativa Nov. 2015 (T2_ISS10_r1.0) GCA_001447565.1 net Trichinella_nelsoni Trichinella nelsoni Nov. 2015 (T7_ISS37_r1.0) GCA_001447455.1 net Trichinella_papuae Trichinella papuae Nov. 2015 (T10_ISS1980_r1.0) GCA_001447755.1 net Trichinella_patagoniensis Trichinella patagoniensis Nov. 2015 (T12_ISS2496_r1.0) GCA_001447655.1 net Trichinella_pseudospiralis Trichinella pseudospiralis Nov. 2015 (T4_ISS588_r1.0) GCA_001447725.1 net Trichinella_spiralis Trichinella spiralis Jan. 2011 (Trichinella_spiralis-3.7.1) GCF_000181795.1 net Trichinella_zimbabwensis Trichinella zimbabwensis Nov. 2015 (T11_ISS1029_r1.0) GCA_001447665.1 net Trichuris_muris Trichuris muris Mar. 2014 (TMUE2.2) GCA_000612645.1 net Trichuris_trichiura Trichuris trichiura Mar. 2014 (TTRE2.1) GCA_000613005.1 net Whipworm Trichuris suis Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1) Jul. 2014 (WS243/T. suis DCEP-RM93M male/triSui1) net Wuchereria_bancrofti Wuchereria bancrofti Feb. 2016 (Wb_PNG_Genome_assembly_pt22) GCA_001555675.1 net
Table 1. Genome assemblies included in the 135-way Conservation track.
The track configuration options allow the user to display the three different sets of scores by all, subclass, individually, or any combination of these. In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the value of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.
Pairwise alignments of each species to the $organism genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.
Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). Note that excluding species from the pairwise display does not alter the the conservation score display.
To view detailed information about the alignments at a specific position, zoom the display in to 30,000 or fewer bases, then click on the alignment.
The Display chains between alignments configuration option enables display of gaps between alignment blocks in the pairwise alignments in a manner similar to the Chain track display. The following conventions are used:
Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:
When zoomed-in to the base-level display, the track shows the base composition of each alignment. The numbers and symbols on the Gaps line indicate the lengths of gaps in the $organism sequence at those alignment positions relative to the longest non-$organism sequence. If there is sufficient space in the display, the size of the gap is shown. If the space is insufficient and the gap size is a multiple of 3, a "*" is displayed; other gap sizes are indicated by "+".
Codon translation is available in base-level display mode if the displayed region is identified as a coding segment. To display this annotation, select the species for translation from the pull-down menu in the Codon Translation configuration section at the top of the page. Then, select one of the following modes:
Codon translation uses the following gene tracks as the basis for translation, depending on the species chosen (Table 2).
Table 2. Gene tracks used for codon translation.
Gene Track Species Ensembl Genes v92 C. elegans, Ciona intestinalis WormBase WS245 genes C. angaria, C. japonica, C. briggsae, C. sp. 5 ju800, C. remanei, C. brenneri, C. tropicalis, P. exspectatus, P. pacificus, Pine wood nematode, N. americanus, A. ceylanicum, Pig roundworm, Barber pole worm, Whipworm, Microworm, Filarial worm, Dog heartworm, O. volvulus, Eye worm, M. incognita, M. hapla, H. bacteriophora/m31e, Trichinella no annotations all others
Pairwise alignments with the $organism genome were generated for each species using lastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. Please note the specific parameters for the alignments. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.
The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.
Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The all species tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 135-way alignment (msa_view). The 4d sites were derived from the NCBI RefSeq gene set, filtered to select single-coverage long transcripts.
This same tree model was used in the phyloP calculations, however their background frequencies were modified to maintain reversibility. The resulting tree model for all species.
The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005.
The phastCons parameters used were: expected-length=45, target-coverage=0.3, rho=0.3.
The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements ( http://compgen.cshl.edu/phast/). Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).
The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".
This track was created using the following programs:
The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community as of March 2007.
Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823
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. PMID: 16024819; PMC: PMC1182216
Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.
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