Description

This track shows multiple alignments of 369 bacteria, 362 Staphylococcus aureus, one Bacillus subtilis and six Escherichia coli, and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 369 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.

Download data available at: hgdownload-test.

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).

Organism
NCBI assembly
SpeciesAssembly namebrowser or
NCBI source
Staph/GCF_000013465.1
reference sequence
Staphylococcus aureus Feb. 2006 (USA300_FPR3757/staAur2) Feb. 2006 (USA300_FPR3757/staAur2)
***** % 99 reference identity *****
Sa_USA300_SUR15Staphylococcus aureus Feb. 2017 (ASM200068v1) GCF_002000685.1
Sa_USA300_SUR24Staphylococcus aureus Feb. 2017 (ASM200086v1) GCF_002000865.1
***** % 98 reference identity *****
Sa_USA300_SUR9Staphylococcus aureus Feb. 2017 (ASM200056v1) GCF_002000565.1
Sa_USA300_SUR10Staphylococcus aureus Feb. 2017 (ASM200058v1) GCF_002000585.1
Sa_USA300_SUR11Staphylococcus aureus Feb. 2017 (ASM200060v1) GCF_002000605.1
Sa_USA300_SUR4Staphylococcus aureus Feb. 2017 (ASM359542v1) GCF_003595425.1
Sa_USA300_SUR8Staphylococcus aureus Feb. 2017 (ASM359550v1) GCF_003595505.1
Sa_USA300_NRS384Staphylococcus aureus subsp. aureus USA300 Mar. 2018 (ASM299386v1) GCF_002993865.1
Sa_1971C01Staphylococcus aureus subsp. aureus Feb. 2018 (ASM171768v3) GCF_001717685.1
Sa_USA300_SUR13Staphylococcus aureus Feb. 2017 (ASM200064v1) GCF_002000645.1
Sa_USA300_SUR21Staphylococcus aureus Feb. 2017 (ASM200080v1) GCF_002000805.1
Sa_USA300_SUR3Staphylococcus aureus Feb. 2017 (ASM359540v1) GCF_003595405.1
Sa_USA300_SUR6Staphylococcus aureus Feb. 2017 (ASM359546v1) GCF_003595465.1
Sa_USA300_SUR7Staphylococcus aureus Feb. 2017 (ASM359548v1) GCF_003595485.1
Sa_USA300_TCH1516Staphylococcus aureus subsp. aureus USA300_TCH1516 Mar. 2009 (ASM1708v1) GCF_000017085.1
Sa_AR_0216Staphylococcus aureus Jun. 2018 (ASM319372v1) GCF_003193725.1
Sa_USA300_SUR14Staphylococcus aureus Feb. 2017 (ASM200066v1) GCF_002000665.1
Sa_USA300_SUR16Staphylococcus aureus Feb. 2017 (ASM200070v1) GCF_002000705.1
Sa_USA300_SUR17Staphylococcus aureus Feb. 2017 (ASM200072v1) GCF_002000725.1
Sa_USA300_SUR18Staphylococcus aureus Feb. 2017 (ASM200074v1) GCF_002000745.1
Sa_USA300_SUR19Staphylococcus aureus Feb. 2017 (ASM200076v1) GCF_002000765.1
Sa_USA300_SUR20Staphylococcus aureus Feb. 2017 (ASM200078v1) GCF_002000785.1
Sa_USA300_SUR22Staphylococcus aureus Feb. 2017 (ASM200082v1) GCF_002000825.1
Sa_USA300_SUR23Staphylococcus aureus Feb. 2017 (ASM200084v1) GCF_002000845.1
Sa_USA300_ISMMS1Staphylococcus aureus USA300-ISMMS1 Feb. 2014 (ASM56845v1) GCF_000568455.1
Sa_UTSW_MRSA_55Staphylococcus aureus Mar. 2016 (ASM158051v1) GCF_001580515.1
Sa_USA300_SUR12Staphylococcus aureus Feb. 2017 (ASM200062v1) GCF_002000625.1
Sa_1625CO1Staphylococcus aureus subsp. aureus Dec. 2017 (ASM171772v2) GCF_001717725.1
Sa_AR_0226Staphylococcus aureus Jun. 2018 (ASM320359v1) GCF_003203595.1
Sa_29b_MRSAStaphylococcus aureus Jan. 2015 (ASM81504v1) GCF_000815045.1
Sa_31b_MRSAStaphylococcus aureus Jan. 2015 (ASM81508v1) GCF_000815085.1
Sa_33bStaphylococcus aureus Jan. 2015 (ASM81512v1) GCF_000815125.1
Sa_26b_MRSAStaphylococcus aureus Jan. 2015 (ASM81516v1) GCF_000815165.1
Sa_25b_MRSAStaphylococcus aureus Jan. 2015 (ASM81520v1) GCF_000815205.1
Sa_27b_MRSAStaphylococcus aureus Jan. 2015 (ASM81524v1) GCF_000815245.1
Sa_UA_S391_USA300Staphylococcus aureus May 2014 (ASM69587v1) GCF_000695875.1
Sa_C2406Staphylococcus aureus Apr. 2017 (ASM208899v1) GCF_002088995.1
Sa_CITStaphylococcus aureus subsp. aureus Apr. 2018 (ASM307339v1) GCF_003073395.1
Sa_OXLIMStaphylococcus aureus subsp. aureus Apr. 2018 (ASM307343v1) GCF_003073435.1
Sa_JE2Staphylococcus aureus Apr. 2017 (ASM208552v1) GCF_002085525.1
Sa_1969NStaphylococcus aureus subsp. aureus Jan. 2018 (ASM171770v2) GCF_001717705.1
Sa_3020C01Staphylococcus aureus subsp. aureus Jan. 2018 (ASM173565v2) GCF_001735655.2
Sa_USA300_2014C02Staphylococcus aureus subsp. aureus Jan. 2018 (ASM118372v2) GCF_001183725.2
Sa_USA300_SUR1_aStaphylococcus aureus subsp. aureus Jan. 2017 (ASM195681v1) GCF_001956815.1
Sa_USA300_SUR1_bStaphylococcus aureus Feb. 2017 (ASM359536v1) GCF_003595365.1
Sa_USA300_SUR2Staphylococcus aureus Feb. 2017 (ASM359538v1) GCF_003595385.1
Sa_FDAARGOS_140Staphylococcus aureus Mar. 2018 (ASM147171v2) GCF_001471715.2
Sa_2148C01Staphylococcus aureus subsp. aureus Jan. 2018 (ASM171797v3) GCF_001717975.2
Sa_USA300_2014C01Staphylococcus aureus subsp. aureus Feb. 2018 (ASM118370v3) GCF_001183705.3
***** % 97 reference identity *****
Sa_5118NStaphylococcus aureus subsp. aureus Feb. 2018 (ASM171764v3) GCF_001717645.1
Sa_CA15Staphylococcus aureus Jun. 2015 (ASM102189v1) GCF_001021895.1
Sa_AR_0223Staphylococcus aureus Jun. 2018 (ASM319368v1) GCF_003193685.1
Sa_CARStaphylococcus aureus subsp. aureus Apr. 2018 (ASM307341v1) GCF_003073415.1
Sa_HUV05Staphylococcus aureus Oct. 2015 (ASM104599v2) GCF_001045995.2
Sa_2395_USA500Staphylococcus aureus Aug. 2014 (ASM74650v1) GCF_000746505.1
Sa_M1Staphylococcus aureus M1 Apr. 2013 (ASM36774v1) GCF_000367745.1
Sa_OC8Staphylococcus aureus Oct. 2016 (ASM235535v1) GCF_002355355.1
Sa_199Staphylococcus aureus Aug. 2018 (ASM342554v1) GCF_003425545.1
Sa_64Staphylococcus aureus Aug. 2018 (ASM342591v1) GCF_003425915.1
***** % 96 reference identity *****
Sa_AR_0225Staphylococcus aureus Jun. 2018 (ASM319396v1) GCF_003193965.1
Sa_EDCC5458Staphylococcus aureus subsp. aureus Nov. 2017 (ASM278646v1) GCF_002786465.1
Sa_NCTC13394Staphylococcus aureus Jun. 2018 (40677_F01) GCF_900474525.1
Sa_28Staphylococcus aureus Aug. 2018 (ASM342583v1) GCF_003425835.1
Sa_82Staphylococcus aureus Aug. 2018 (ASM342588v1) GCF_003425885.1
Sa_SVH7513Staphylococcus aureus May 2018 (ASM311172v1) GCF_003111725.1
Sa_NRS120Staphylococcus aureus Jan. 2018 (ASM101948v2) GCF_001019485.2
Sa_V2200Staphylococcus aureus Oct. 2015 (ASM104609v2) GCF_001046095.2
Sa_MIStaphylococcus aureus Jan. 2016 (ASM154841v1) GCF_001548415.1
Sa_TCH_959Staphylococcus aureus Jan. 2018 (ASM101868v2) GCF_001018685.2
Sa_COLStaphylococcus aureus subsp. aureus COL May 2005 (ASM1204v1) GCF_000012045.1
Sa_FDAARGOS_5Staphylococcus aureus subsp. aureus Feb. 2018 (ASM62661v3) GCF_000626615.2
Sa_NCTC13140Staphylococcus aureus Jun. 2018 (40677_A01) GCF_900474725.1
Sa_Gv88Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151570v1) GCF_001515705.1
Sa_Gv51Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151566v1) GCF_001515665.1
***** % 95 reference identity *****
Sa_164Staphylococcus aureus Aug. 2018 (ASM335488v1) GCF_003354885.1
Sa_HC1335Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151576v1) GCF_001515765.1
Sa_Gv69Staphylococcus aureus subsp. aureus Oct. 2014 (ASM76957v1) GCF_000769575.1
Sa_JMUB3031Staphylococcus aureus Aug. 2018 (ASM357383v1) GCF_003573835.1
Sa_Be62Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151568v1) GCF_001515685.1
Sa_HC1340Staphylococcus aureus subsp. aureus Jan. 2016 (ASM151574v1) GCF_001515745.1
Sa_Bmb9393Staphylococcus aureus Jul. 2013 (ASM41834v1) GCF_000418345.1
Sa_USA400_0051Staphylococcus aureus Nov. 2017 (ASM279528v1) GCF_002795285.1
Sa_UCI62Staphylococcus aureus subsp. aureus Jan. 2017 (ASM197500v1) GCF_001975005.1
Sa_AR_0468Staphylococcus aureus Jun. 2018 (ASM320361v1) GCF_003203615.1
Sa_AR_0467Staphylococcus aureus Jun. 2018 (ASM319388v1) GCF_003193885.1
Sa_JH1Staphylococcus aureus subsp. aureus JH1 Jun. 2007 (ASM1712v1) GCF_000017125.1
Sa_AR_474Staphylococcus aureus Jul. 2018 (ASM333090v1) GCF_003330905.1
Sa_AR465Staphylococcus aureus Apr. 2018 (ASM307365v1) GCF_003073655.1
Sa_JH9Staphylococcus aureus subsp. aureus JH9 May 2007 (ASM1680v1) GCF_000016805.1
Sa_HPV107Staphylococcus aureus Jan. 2018 (ASM101957v2) GCF_001019575.2
Sa_AR_0215Staphylococcus aureus Jun. 2018 (ASM319402v1) GCF_003194025.1
Sa_ZJ5499Staphylococcus aureus May 2016 (ASM164088v1) GCF_001640885.1
Sa_Sa_Newman_UoMStaphylococcus aureus Jul. 2016 (Sa_Newman_UoM) GCF_900092595.1
Sa_NewmanStaphylococcus aureus subsp. aureus str. Newman Jul. 2007 (ASM1046v1) GCF_000010465.1
Sa_Newman_D2CStaphylococcus aureus subsp. aureus Sep. 2017 (ASM231039v1) GCF_002310395.1
Sa_Newman_NYU_NewmanStaphylococcus aureus subsp. aureus str. Newman Sep. 2017 (ASM231043v1) GCF_002310435.1
Sa_AR461Staphylococcus aureus Apr. 2018 (ASM307371v1) GCF_003073715.1
Sa_NRS271Staphylococcus aureus Jan. 2018 (ASM101883v2) GCF_001018835.2
Sa_SA112Staphylococcus aureus Apr. 2018 (ASM302966v1) GCF_003029665.1
Sa_FDAARGOS_412Staphylococcus aureus Sep. 2017 (ASM238624v1) GCF_002386245.1
Sa_NCTC9944Staphylococcus aureus Jun. 2018 (40415_F02) GCF_900474575.1
Sa_545Staphylococcus aureus Aug. 2018 (ASM335494v1) GCF_003354945.1
Sa_MSSA54Staphylococcus aureus Nov. 2018 (ASM379818v1) GCF_003798185.1
Sa_FDAARGOS_43Staphylococcus aureus Feb. 2018 (ASM101912v2) GCF_001019125.2
Sa_Mw2_2018Staphylococcus aureus Jan. 2018 (ASM101953v2) GCF_001019535.2
Sa_FCFHV36Staphylococcus aureus Apr. 2015 (ASM96922v1) GCF_000969225.1
Sa_MW2_2004Staphylococcus aureus subsp. aureus MW2 May 2004 (ASM1126v1) GCF_000011265.1
Sa_546Staphylococcus aureus Aug. 2018 (ASM335496v1) GCF_003354965.1
Sa_FDAARGOS_1Staphylococcus aureus Feb. 2018 (ASM101925v2) GCF_001019255.2
Sa_54Staphylococcus aureus Aug. 2018 (ASM335480v1) GCF_003354805.1
Sa_T0131Staphylococcus aureus subsp. aureus T0131 Apr. 2011 (ASM20466v1) GCF_000204665.1
Sa_165Staphylococcus aureus Aug. 2018 (ASM335466v1) GCF_003354665.1
Sa_FDAARGOS_48Staphylococcus aureus Feb. 2018 (ASM101920v2) GCF_001019205.2
Sa_NCTC13277Staphylococcus aureus Jun. 2018 (35910_A02) GCF_900478245.1
Sa_MRSA252Staphylococcus aureus subsp. aureus MRSA252 Jun. 2004 (ASM1150v1) GCF_000011505.1
Sa_WCH_SK2Staphylococcus aureus Aug. 2018 (ASM339410v1) GCF_003394105.1
***** % 94 reference identity *****
Sa_H_EMRSA_15Staphylococcus aureus subsp. aureus May 2014 (ASM69521v1) GCF_000695215.1
Sa_MRSA107Staphylococcus aureus Jan. 2018 (ASM289538v1) GCF_002895385.1
Sa_V521Staphylococcus aureus May 2016 (ASM164102v1) GCF_001641025.1
Sa_GR2Staphylococcus aureus subsp. aureus Sep. 2015 (ASM129698v1) GCF_001296985.1
Sa_NMR08Staphylococcus aureus Oct. 2017 (ASM240710v1) GCF_002407105.1
Sa_NCTC13395Staphylococcus aureus Jun. 2018 (40871_F01) GCF_900474735.1
Sa_NZAK3Staphylococcus aureus Jan. 2016 (NZAK3) GCF_900017775.1
Sa_AR_0472Staphylococcus aureus Jun. 2018 (ASM319366v1) GCF_003193665.1
Sa_11819_97Staphylococcus aureus subsp. aureus 11819-97 Dec. 2011 (ASM23923v1) GCF_000239235.1
Sa_NCTC13435Staphylococcus aureus Mar. 2015 (NCTC13435) GCF_001457495.1
Sa_JKD6008Staphylococcus aureus subsp. aureus str. JKD6008 Aug. 2010 (ASM14559v1) GCF_000145595.1
Sa_AR_0473Staphylococcus aureus Jun. 2018 (ASM319378v1) GCF_003193785.1
Sa_NCCP14562Staphylococcus aureus May 2016 (ASM164092v1) GCF_001640925.1
Sa_NCCP14558Staphylococcus aureus May 2016 (ASM164090v1) GCF_001640905.1
Sa_HO_5096_0412Staphylococcus aureus subsp. aureus HO 5096 0412 Apr. 2012 (ASM28453v1) GCF_000284535.1
Sa_JKD6159Staphylococcus aureus subsp. aureus JKD6159 Aug. 2010 (ASM14495v1) GCF_000144955.1
Sa_AR_0219Staphylococcus aureus Jun. 2018 (ASM319370v1) GCF_003193705.1
Sa_Mu50Staphylococcus aureus subsp. aureus Mu50 May 2004 (ASM966v1) GCF_000009665.1
Sa_MOZ66Staphylococcus aureus Aug. 2018 (ASM342614v1) GCF_003426145.1
Sa_ED98Staphylococcus aureus subsp. aureus ED98 Oct. 2009 (ASM2458v1) GCF_000024585.1
Sa_Z172Staphylococcus aureus subsp. aureus Z172 Oct. 2013 (ASM48588v1) GCF_000485885.1
Sa_M121Staphylococcus aureus Jun. 2015 (ASM102187v1) GCF_001021875.1
Sa_TW20Staphylococcus aureus subsp. aureus TW20 Nov. 2009 (ASM2704v1) GCF_000027045.1
Sa_CA12Staphylococcus aureus Oct. 2015 (ASM104579v2) GCF_001045795.2
Sa_FORC_027Staphylococcus aureus Sep. 2016 (ASM172596v1) GCF_001725965.1
Sa_MSSA476Staphylococcus aureus subsp. aureus MSSA476 Jun. 2004 (ASM1152v1) GCF_000011525.1
Sa_FDAARGOS_2Staphylococcus aureus Feb. 2018 (ASM101864v2) GCF_001018645.2
Sa_FORC_062Staphylococcus aureus Aug. 2018 (ASM335192v1) GCF_003351925.1
Sa_AR_0228Staphylococcus aureus Jun. 2018 (ASM320363v1) GCF_003203635.1
Sa_187Staphylococcus aureus Aug. 2018 (ASM335456v1) GCF_003354565.1
Sa_629Staphylococcus aureus Aug. 2018 (ASM335458v1) GCF_003354585.1
Sa_FDAARGOS_40Staphylococcus aureus Feb. 2018 (ASM101949v2) GCF_001019495.2
Sa_61Staphylococcus aureus Aug. 2018 (ASM335470v1) GCF_003354705.1
Sa_191Staphylococcus aureus Aug. 2018 (ASM335476v1) GCF_003354765.1
Sa_628Staphylococcus aureus Aug. 2018 (ASM335498v1) GCF_003354985.1
Sa_UCI_28_ST5Staphylococcus aureus subsp. aureus Jan. 2017 (ASM197504v1) GCF_001975045.1
Sa_CMRSA_3Staphylococcus aureus Jun. 2018 (ASM326477v1) GCF_003264775.1
Sa_ClinicalStaphylococcus aureus subsp. aureus Dec. 2016 (PP_HGAG_QV30_2SC_T4) GCF_900129335.1
Sa_17_LA_343Staphylococcus aureus Jul. 2018 (17_LA_343) GCF_900324345.1
Sa_Mu3Staphylococcus aureus subsp. aureus Mu3 Sep. 2007 (ASM1044v1) GCF_000010445.1
Sa_AR_0220Staphylococcus aureus Jun. 2018 (ASM320367v1) GCF_003203675.1
Sa_NRS1Staphylococcus aureus Jan. 2018 (ASM101943v2) GCF_001019435.2
Sa_ISU935_ST5Staphylococcus aureus Jun. 2017 (ASM220455v1) GCF_002204555.1
Sa_CR14_035Staphylococcus aureus Apr. 2018 (ASM303146v1) GCF_003031465.1
Sa_ST228_16125Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM38298v1) GCF_000382985.1
Sa_MN8Staphylococcus aureus subsp. aureus MN8 Jun. 2010 (ASM16019v1) GCF_000160195.1
Sa_04_02981Staphylococcus aureus 04-02981 Nov. 2010 (ASM2514v1) GCF_000025145.1
Sa_N315Staphylococcus aureus subsp. aureus N315 May 2004 (ASM964v1) GCF_000009645.1
Sa_NRS484Staphylococcus aureus Jan. 2018 (ASM101939v2) GCF_001019395.2
Sa_CA_347Staphylococcus aureus CA-347 Jun. 2013 (ASM41277v1) GCF_000412775.1
Sa_7_4623Staphylococcus aureus Jul. 2018 (7_4623) GCF_900324225.1
Sa_HOU1444_VRStaphylococcus aureus Sep. 2015 (ASM127874v1) GCF_001278745.1
Sa_FORC_045Staphylococcus aureus Jun. 2017 (ASM220932v1) GCF_002209325.1
Sa_DSM_20231Staphylococcus aureus subsp. aureus DSM 20231 Jun. 2015 (ASM102710v1) GCF_001027105.1
Sa_9_LA_281Staphylococcus aureus Jul. 2018 (9_LA_281) GCF_900324265.1
Sa_NCTC11940Staphylococcus aureus Jun. 2018 (42197_E02) GCF_900475055.1
Sa_NRS70Staphylococcus aureus Jan. 2018 (ASM101930v2) GCF_001019305.2
Sa_AR462Staphylococcus aureus Apr. 2018 (ASM307377v1) GCF_003073775.1
Sa_0201753_2Staphylococcus aureus Jun. 2018 (ASM319418v1) GCF_003194185.1
Sa_CFSAN007850Staphylococcus aureus Oct. 2017 (ASM263380v1) GCF_002633805.1
Sa_NCTC6136Staphylococcus aureus Jun. 2018 (41004_D01) GCF_900474715.1
Sa_1_1439Staphylococcus aureus Jul. 2018 (1_1439) GCF_900324205.1
Sa_RIVM6519Staphylococcus aureus Apr. 2016 (ASM161830v1) GCF_001618305.1
Sa_CHU15_056Staphylococcus aureus Jun. 2018 (ASM319440v1) GCF_003194405.1
***** % 93 reference identity *****
Sa_ch22Staphylococcus aureus Jul. 2018 (ASM335060v1) GCF_003350605.1
Sa_22_LA_562Staphylococcus aureus Jul. 2018 (22_LA_562) GCF_900324415.1
Sa_ch21Staphylococcus aureus Jul. 2018 (ASM334315v1) GCF_003343155.1
Sa_M92Staphylococcus aureus Jun. 2018 (ASM209759v2) GCF_002097595.2
Sa_5_3949Staphylococcus aureus Jul. 2018 (5_3949) GCF_900324235.1
Sa_FORC_039Staphylococcus aureus May 2017 (ASM214011v1) GCF_002140115.1
Sa_CFSAN007896Staphylococcus aureus Apr. 2018 (ASM303142v1) GCF_003031425.1
Sa_FORC_012Staphylococcus aureus Mar. 2016 (ASM158049v1) GCF_001580495.1
Sa_JH4899Staphylococcus aureus Mar. 2017 (ASM235667v1) GCF_002356675.1
Sa_CN1Staphylococcus aureus subsp. aureus CN1 Aug. 2013 (ASM46305v1) GCF_000463055.1
Sa_SR434Staphylococcus aureus Feb. 2017 (ASM198613v1) GCF_001986135.1
Sa_CC5Staphylococcus aureus Apr. 2018 (ASM303148v1) GCF_003031485.1
Sa_FDAARGOS_159Staphylococcus aureus Feb. 2018 (ASM155879v2) GCF_001558795.2
Sa_12_LA_293Staphylococcus aureus Jul. 2018 (12_LA_293) GCF_900324315.1
Sa_FORC_040Staphylococcus aureus Jul. 2017 (ASM221466v1) GCF_002214665.1
Sa_NRS153Staphylococcus aureus Jan. 2018 (ASM101884v2) GCF_001018845.2
Sa_FORC_001Staphylococcus aureus subsp. aureus Nov. 2014 (ASM77202v1) GCF_000772025.1
Sa_15_LA_305Staphylococcus aureus Jul. 2018 (15_LA_305) GCF_900324335.1
Sa_FDAARGOS_504Staphylococcus aureus Nov. 2018 (ASM382791v1) GCF_003827915.1
Sa_TMUS2126Staphylococcus aureus subsp. aureus Mar. 2015 (ASM154965v1) GCF_001549655.1
Sa_TMUS2134Staphylococcus aureus subsp. aureus Mar. 2015 (ASM154967v1) GCF_001549675.1
Sa_CFSAN064038Staphylococcus aureus Apr. 2018 (ASM302964v1) GCF_003029645.1
Sa_13_LA_301Staphylococcus aureus Jul. 2018 (13_LA_301) GCF_900324305.1
Sa_14_5418Staphylococcus aureus Jul. 2018 (14_5418) GCF_900324325.1
Sa_SA564Staphylococcus aureus Sep. 2015 (ASM128114v1) GCF_001281145.1
Sa_21_LA_436Staphylococcus aureus Jul. 2018 (21_LA_436) GCF_900324405.1
Sa_8_LA_272Staphylococcus aureus Jul. 2018 (8_LA_272) GCF_900324245.1
Sa_20_LA_415Staphylococcus aureus Jul. 2018 (20_LA_415) GCF_900324385.1
Sa_AR_0470Staphylococcus aureus Jun. 2018 (ASM319374v1) GCF_003193745.1
Sa_ED133Staphylococcus aureus subsp. aureus ED133 Jun. 2010 (ASM21031v1) GCF_000210315.1
Sa_TCH60Staphylococcus aureus subsp. aureus TCH60 Nov. 2010 (ASM15953v2) GCF_000159535.2
Sa_2_LA_86Staphylococcus aureus Jul. 2018 (2_LA_86) GCF_900324255.1
Sa_3_LA_115Staphylococcus aureus Jul. 2018 (3_LA_115) GCF_900324215.1
Sa_ECT_R_2Staphylococcus aureus subsp. aureus ECT-R 2 Nov. 2010 (ASM25313v1) GCF_000253135.1
Sa_19_LA_388Staphylococcus aureus Jul. 2018 (19_LA_388) GCF_900324365.1
Sa_6_LA_232Staphylococcus aureus Jul. 2018 (6_LA_232) GCF_900324275.1
Sa_MOK063Staphylococcus aureus Jun. 2018 (ASM318610v1) GCF_003186105.1
Sa_CFSAN018749Staphylococcus aureus Apr. 2018 (ASM303006v1) GCF_003030065.1
Sa_2148NStaphylococcus aureus subsp. aureus Jan. 2018 (ASM171766v2) GCF_001717665.1
Sa_NCTC10344Staphylococcus aureus Jun. 2018 (41236_E02) GCF_900474755.1
Sa_MOK042Staphylococcus aureus Jun. 2018 (ASM318612v1) GCF_003186125.1
Sa_CFSAN007851Staphylococcus aureus Oct. 2017 (ASM263382v1) GCF_002633825.1
Sa_E16SA093Staphylococcus aureus Jul. 2018 (ASM334273v1) GCF_003342735.1
Sa_ST228_16035Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM38296v1) GCF_000382965.1
Sa_ST228_10388Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96732v1) GCF_000967325.1
Sa_ST228_10497Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96734v1) GCF_000967345.1
Sa_ST228_15532Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96736v1) GCF_000967365.1
Sa_ST228_18341Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96738v1) GCF_000967385.1
Sa_55_99_44Staphylococcus aureus Dec. 2017 (ASM280388v1) GCF_002803885.1
Sa_ST228_18583Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM38300v1) GCF_000383005.1
Sa_ST228_18412Staphylococcus aureus subsp. aureus ST228 Oct. 2012 (ASM96740v1) GCF_000967405.1
Sa_080880048_3Staphylococcus aureus Jun. 2018 (ASM319406v1) GCF_003194065.1
Sa_101110051_1Staphylococcus aureus Jun. 2018 (ASM319414v1) GCF_003194145.1
Sa_FDA209PStaphylococcus aureus Sep. 2015 (ASM154829v1) GCF_001548295.1
Sa_ATCC_6538Staphylococcus aureus subsp. aureus Mar. 2017 (ASM202514v1) GCF_002025145.1
Sa_SA268Staphylococcus aureus subsp. aureus SA268 Aug. 2014 (ASM73761v1) GCF_000737615.1
Sa_CMRSA_6Staphylococcus aureus Jun. 2018 (ASM326481v1) GCF_003264815.1
Sa_XQStaphylococcus aureus Nov. 2015 (ASM144434v1) GCF_001444345.1
Sa_CFSAN007847Staphylococcus aureus Oct. 2017 (ASM263378v1) GCF_002633785.1
Sa_78Staphylococcus aureus Aug. 2018 (ASM335490v1) GCF_003354905.1
Sa_BA01611Staphylococcus aureus Mar. 2017 (ASM129832v2) GCF_001298325.2
Sa_ST772_MRSA_V_DAR4145Staphylococcus aureus subsp. aureus ST772-MRSA-V Jan. 2015 (ASM82803v1) GCF_000828035.1
Sa_AR_0469Staphylococcus aureus Jun. 2018 (ASM319400v1) GCF_003194005.1
Sa_FORC_061Staphylococcus aureus Jul. 2018 (ASM334705v1) GCF_003347055.1
Sa_ST398_S0385Staphylococcus aureus subsp. aureus ST398 Jan. 2010 (ASM958v1) GCF_000009585.1
Sa_QD_CD9Staphylococcus aureus Aug. 2018 (ASM343236v1) GCF_003432365.1
Sa_S_aureus_171Staphylococcus aureus Apr. 2018 (171) GCF_900240125.1
Sa_101110041_3Staphylococcus aureus Jun. 2018 (ASM319416v1) GCF_003194165.1
Sa_O17Staphylococcus aureus Sep. 2018 (ASM349012v1) GCF_003490125.1
Sa_AR_475Staphylococcus aureus Jul. 2018 (ASM328839v1) GCF_003288395.1
Sa_NRS143Staphylococcus aureus Jan. 2018 (ASM101897v2) GCF_001018975.2
Sa_SA40TWStaphylococcus aureus Nov. 2016 (ASM188026v1) GCF_001880265.1
Sa_GD705Staphylococcus aureus Jul. 2018 (ASM208907v2) GCF_002089075.2
Sa_13420Staphylococcus aureus Jun. 2018 (ASM319410v1) GCF_003194105.1
Sa_CFBR_105Staphylococcus aureus Aug. 2018 (ASM343136v1) GCF_003431365.1
Sa_NCTC13137Staphylococcus aureus Jun. 2018 (40657_E01) GCF_900474555.1
Sa_GN1Staphylococcus aureus Oct. 2017 (ASM360991v1) GCF_003609915.1
Sa_AR464Staphylococcus aureus Apr. 2018 (ASM307375v1) GCF_003073755.1
Sa_277Staphylococcus aureus Aug. 2018 (ASM335468v1) GCF_003354685.1
Sa_85Staphylococcus aureus Aug. 2018 (ASM335478v1) GCF_003354785.1
Sa_F17SA003Staphylococcus aureus Jul. 2018 (ASM334277v1) GCF_003342775.1
Sa_27Staphylococcus aureus Aug. 2018 (ASM335454v1) GCF_003354545.1
Sa_O46Staphylococcus aureus O46 Dec. 2017 (ASM18945v3) GCF_000189455.2
Sa_No10Staphylococcus aureus Jun. 2017 (ASM235665v1) GCF_002356655.1
Sa_08_02300Staphylococcus aureus Jun. 2016 (ASM165607v1) GCF_001656075.1
***** % 92 reference identity *****
Sa_502A_RN6607Staphylococcus aureus Mar. 2014 (ASM59796v1) GCF_000597965.1
Sa_IT1_SStaphylococcus aureus Jun. 2018 (ASM318498v1) GCF_003184985.1
Sa_IT4_RStaphylococcus aureus Jun. 2018 (ASM318500v1) GCF_003185005.1
Sa_CFSAN007894Staphylococcus aureus Oct. 2017 (ASM263386v1) GCF_002633865.1
Sa_RIVM3897Staphylococcus aureus Dec. 2015 (ASM146575v1) GCF_001465755.1
Sa_AR_0471Staphylococcus aureus Jun. 2018 (ASM319376v1) GCF_003193765.1
Sa_FDAARGOS_10Staphylococcus aureus Feb. 2018 (ASM101872v2) GCF_001018725.2
Sa_08_02119Staphylococcus aureus Jun. 2016 (ASM165604v1) GCF_001656045.1
Sa_NX_T55Staphylococcus aureus Aug. 2018 (ASM343234v1) GCF_003432345.1
Sa_NCTC8325_2018Staphylococcus aureus subsp. aureus NCTC 8325 Jun. 2018 (43024_E01) GCF_900475245.1
Sa_HG001_RN1Staphylococcus aureus subsp. aureus Dec. 2016 (ASM190018v1) GCF_001900185.1
Sa_NCTC8325_2006Staphylococcus aureus subsp. aureus NCTC 8325 Feb. 2006 (ASM1342v1) GCF_000013425.1
Sa_O326Staphylococcus aureus Oct. 2018 (ASM362783v1) GCF_003627835.1
Sa_AR466Staphylococcus aureus Apr. 2018 (ASM307363v1) GCF_003073635.1
Sa_ILRI_Eymole1_1Staphylococcus aureus Oct. 2014 (Staphylococcus_aureus_Sa_ILRI_217) GCF_000953255.1
Sa_NRS149Staphylococcus aureus Jan. 2018 (ASM101877v2) GCF_001018775.2
Sa_BB155Staphylococcus aureus Feb. 2016 (BB155) GCF_900004855.1
Sa_Tager_104Staphylococcus aureus subsp. aureus Tager 104 Mar. 2016 (ASM45238v2) GCF_000452385.2
Sa_GD1539Staphylococcus aureus Jul. 2018 (ASM208911v2) GCF_002089115.2
Sa_16_LA_309Staphylococcus aureus Jul. 2018 (16_LA_309) GCF_900324295.1
Sa_SJTUF_J27Staphylococcus aureus Jan. 2017 (ASM195675v1) GCF_001956755.1
Sa_HZW450Staphylococcus aureus Oct. 2017 (ASM244297v1) GCF_002442975.1
Sa_JMUB1273Staphylococcus aureus Aug. 2018 (ASM357385v1) GCF_003573855.1
Sa_121560027_1Staphylococcus aureus Jun. 2018 (ASM319420v1) GCF_003194205.1
Sa_LA_MRSA_ST398_E154Staphylococcus aureus subsp. aureus Nov. 2016 (ASM188707v1) GCF_001887075.1
Sa_45Staphylococcus aureus Aug. 2018 (ASM335486v1) GCF_003354865.1
Sa_135Staphylococcus aureus Aug. 2018 (ASM335492v1) GCF_003354925.1
Sa_PTDrAP2Staphylococcus aureus May 2018 (ASM311174v1) GCF_003111745.1
Sa_FDAARGOS_6Staphylococcus aureus Feb. 2018 (ASM101865v2) GCF_001018655.2
Sa_EDCC5464Staphylococcus aureus subsp. aureus Nov. 2017 (ASM278653v1) GCF_002786535.1
Sa_ISU926_ST398Staphylococcus aureus subsp. aureus Jun. 2017 (ASM220457v1) GCF_002204575.1
Sa_SA957Staphylococcus aureus subsp. aureus SA957 Sep. 2013 (ASM47084v1) GCF_000470845.1
Sa_468Staphylococcus aureus Aug. 2018 (ASM335462v1) GCF_003354625.1
Sa_466Staphylococcus aureus Aug. 2018 (ASM335474v1) GCF_003354745.1
Sa_143Staphylococcus aureus Aug. 2018 (ASM335472v1) GCF_003354725.1
Sa_M013Staphylococcus aureus subsp. aureus M013 Dec. 2011 (ASM23712v1) GCF_000237125.1
Sa_08S00974Staphylococcus aureus Mar. 2017 (ASM202512v1) GCF_002025125.1
Sa_NCTC5663Staphylococcus aureus Jun. 2018 (41004_B01) GCF_900474695.1
Sa_ST20130942Staphylococcus aureus Apr. 2016 (ASM161136v1) GCF_001611365.1
Sa_ST20130943Staphylococcus aureus Apr. 2016 (ASM161138v1) GCF_001611385.1
Sa_NRS107Staphylococcus aureus Jan. 2018 (ASM101927v2) GCF_001019275.2
Sa_RKI4Staphylococcus aureus Jun. 2015 (ASM102704v1) GCF_001027045.1
Sa_JS395Staphylococcus aureus subsp. aureus Oct. 2015 (ASM130723v1) GCF_001307235.1
Sa_422Staphylococcus aureus Aug. 2018 (ASM335460v1) GCF_003354605.1
Sa_128Staphylococcus aureus Aug. 2018 (ASM335464v1) GCF_003354645.1
Sa_24117_WTStaphylococcus aureus Aug. 2018 (24117-WT) GCF_900323905.1
Sa_24117_REVStaphylococcus aureus Aug. 2018 (24117-REV) GCF_900324045.1
Sa_24117_SCVStaphylococcus aureus Aug. 2018 (24117-SCV) GCF_900324065.1
Sa_GN3Staphylococcus aureus Oct. 2017 (ASM360989v1) GCF_003609895.1
Sa_AUS0325Staphylococcus aureus Sep. 2016 (AUS0325) GCF_900096745.1
Sa_ATCC_25923Staphylococcus aureus subsp. aureus Sep. 2014 (ASM75620v1) GCF_000756205.1
Sa_Seattle_1945_G477Staphylococcus aureus Jun. 2017 (ASM220207v1) GCF_002202075.1
Sa_Seattle_1945_G478Staphylococcus aureus Jun. 2017 (ASM220209v1) GCF_002202095.1
Sa_10_5235Staphylococcus aureus Jul. 2018 (10_5235) GCF_900324355.1
Sa_RIVM1295Staphylococcus aureus Dec. 2015 (ASM146563v1) GCF_001465635.1
Sa_4_LA_208Staphylococcus aureus Jul. 2018 (4_LA_208) GCF_900324285.1
Sa_NCTC3761Staphylococcus aureus Jun. 2018 (40961_F01) GCF_900474675.1
Sa_08BA02176Staphylococcus aureus 08BA02176 Sep. 2012 (ASM29659v1) GCF_000296595.1
Sa_GD1677Staphylococcus aureus Jul. 2018 (ASM208909v2) GCF_002089095.2
Sa_1549_WTStaphylococcus aureus Aug. 2018 (1549-WT) GCF_900323925.1
Sa_1549_SCVStaphylococcus aureus Aug. 2018 (1549-SCV) GCF_900323965.1
Sa_1549_REVStaphylococcus aureus Aug. 2018 (1549-REV) GCF_900323955.1
Sa_FDAARGOS_15Staphylococcus aureus Feb. 2018 (ASM101880v2) GCF_001018805.1
Sa_CFSAN007883Staphylococcus aureus Oct. 2017 (ASM263384v1) GCF_002633845.1
***** % 91 reference identity *****
Sa_NCTC8726Staphylococcus aureus Jun. 2018 (41315_B01) GCF_900474565.1
Sa_AR_0222Staphylococcus aureus Jun. 2018 (ASM320365v1) GCF_003203655.1
Sa_FORC_026Staphylococcus aureus Nov. 2016 (ASM187954v1) GCF_001879545.1
Sa_CFSAN064037Staphylococcus aureus Apr. 2018 (ASM303008v1) GCF_003030085.1
Sa_RF122Staphylococcus aureus RF122 Nov. 2005 (ASM900v1) GCF_000009005.1
Sa_GD5Staphylococcus aureus Apr. 2017 (ASM208905v1) GCF_002089055.1
Sa_FORC59Staphylococcus aureus Mar. 2018 (ASM301087v1) GCF_003010875.1
Sa_SA40Staphylococcus aureus subsp. aureus SA40 Sep. 2013 (ASM47086v1) GCF_000470865.1
Sa_LGA251Staphylococcus aureus subsp. aureus LGA251 Aug. 2011 (ASM23726v1) GCF_000237265.1
Sa_293GStaphylococcus aureus Jul. 2018 (ASM208903v2) GCF_002089035.2
Sa_NRS137Staphylococcus aureus Jan. 2018 (ASM101873v2) GCF_001018735.2
Sa_NCTC9752Staphylococcus aureus Jun. 2018 (41236_D02) GCF_900474665.1
Sa_71193Staphylococcus aureus subsp. aureus 71193 Apr. 2012 (ASM25868v1) GCF_000258685.1
Sa_K18Staphylococcus aureus Jan. 2018 (ASM285041v1) GCF_002850415.1
Sa_K5Staphylococcus aureus Feb. 2018 (ASM295201v1) GCF_002952015.1
Sa_RIVM1607Staphylococcus aureus Dec. 2015 (ASM146567v1) GCF_001465675.1
Sa_VC40Staphylococcus aureus subsp. aureus VC40 Feb. 2012 (ASM24549v1) GCF_000245495.1
Sa_NRS133Staphylococcus aureus Jan. 2018 (ASM101891v2) GCF_001018915.2
Sa_NRS146Staphylococcus aureus Jan. 2018 (ASM101941v2) GCF_001019415.2
Sa_ST20130938Staphylococcus aureus Apr. 2016 (ASM161140v1) GCF_001611405.1
Sa_ST20130939Staphylococcus aureus Apr. 2016 (ASM161142v1) GCF_001611425.1
Sa_NCTC7485Staphylococcus aureus Jun. 2018 (40853_C01) GCF_900474535.1
Sa_CFSAN018750Staphylococcus aureus Apr. 2018 (ASM303022v1) GCF_003030225.1
Sa_55_2053Staphylococcus aureus subsp. aureus 55/2053 Aug. 2013 (ASM16033v2) GCF_000160335.2
Sa_80wphwpl_v1Staphylococcus aureus Dec. 2018 (ASM385557v1) GCF_003855575.1
Sa_6850Staphylococcus aureus subsp. aureus 6850 Aug. 2013 (ASM46295v1) GCF_000462955.1
***** % 90 reference identity *****
Sa_MCRF184Staphylococcus aureus Mar. 2016 (ASM159420v1) GCF_001594205.1
Sa_K17Staphylococcus aureus Jan. 2018 (ASM285039v1) GCF_002850395.1
Sa_ST20130940Staphylococcus aureus Apr. 2016 (ASM161132v1) GCF_001611325.1
Sa_ST20130941Staphylococcus aureus Apr. 2016 (ASM161134v1) GCF_001611345.1
Sa_CFSAN007835Staphylococcus aureus Oct. 2017 (ASM263376v1) GCF_002633765.1
***** % 88 reference identity *****
Sa_MS4Staphylococcus aureus Dec. 2015 (ASM145621v1) GCF_001456215.1
***** others *****
Bacillus_subtilis_168Bacillus subtilis subsp. subtilis str. 168 Mar. 2009 (ASM904v1) GCF_000009045.1
E_coli_K_12_MG1655Escherichia coli str. K-12 substr. MG1655 Sep. 2013 (ASM584v2) GCF_000005845.2
E_coli_O157_H7_Sakai_RIMD_0509952Escherichia coli O157:H7 str. Sakai Jun. 2018 (ASM886v2) GCF_000008865.2
E_coli_UMN026Escherichia coli UMN026 Dec. 2008 (ASM2632v1) GCF_000026325.1
E_coli_O83_H1_NRG_857CEscherichia coli O83:H1 str. NRG 857C Nov. 2010 (ASM18334v1) GCF_000183345.1
E_coli_IAI39Escherichia coli IAI39 Dec. 2008 (ASM2634v1) GCF_000026345.1
E_coli_O104_H4_2011C_3493Escherichia coli O104:H4 str. 2011C-3493 Sep. 2012 (ASM29945v1) GCF_000299455.1

Table 1. Genome assemblies included in the 369-way Conservation track.

Downloads for data in this track are available:

Display Conventions and Configuration

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.

Gap Annotation

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:

Genomic Breaks

Discontinuities in the genomic context (chromosome, scaffold or region) of the aligned DNA in the aligning species are shown as follows:

Base Level

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).

Gene TrackSpecies
NCBI RefSeq genesall 369 genome sequences
Table 2. Gene tracks used for codon translation.

Methods

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.

Phylogenetic Tree Model

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 369-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.

PhastCons Conservation

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.

PhyloP Conservation

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).

Conserved Elements

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".

Credits

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.

References

Phylo-HMMs, phastCons, and phyloP:

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.

Yang Z. A space-time process model for the evolution of DNA sequences. Genetics. 1995 Feb;139(2):993-1005. PMID: 7713447; PMC: PMC1206396

Chain/Net:

Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784

Multiz:

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, et al. Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 2004 Apr;14(4):708-15. PMID: 15060014; PMC: PMC383317

Lastz (formerly Blastz):

Chiaromonte F, Yap VB, Miller W. Scoring pairwise genomic sequence alignments. Pac Symp Biocomput. 2002:115-26. PMID: 11928468

Harris RS. Improved pairwise alignment of genomic DNA. Ph.D. Thesis. Pennsylvania State University, USA. 2007.

Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961

Phylogenetic Tree:

Bernard G, Ragan MA, Chan CX. Recapitulating phylogenies using k-mers: from trees to networks. F1000Res. 2016;5:2789. PMID: 28105314

Fan H, Ives AR, Surget-Groba Y, Cannon CH. An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data. BMC Genomics. 2015;16(1):522. PMID: 26169061

Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, Springer MS. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 2001 Dec 14;294(5550):2348-51. PMID: 11743200