27a34b2d1472b7a8dc28631fa09423dc875b1153 hiram Thu Sep 19 12:44:12 2024 -0700 BRC update refs #34337 diff --git src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt index 3e2e091..0b88064 100644 --- src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt +++ src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt @@ -1,107 +1,118 @@ GCA_000001905.1_Loxafr3.0 mammals GCA_000001985.1_JCVI-PMFA1-2.0 fungi GCA_000002305.1_EquCab2.0 mammals GCA_000002525.1_ASM252v1 fungi GCA_000002545.2_ASM254v2 fungi GCA_000002595.3_Chlamydomonas_reinhardtii_v5.5 plants GCA_000002725.2_ASM272v2 invertebrate GCA_000002765.3_GCA_000002765 invertebrate GCA_000002875.2_ASM287v2 invertebrate +GCA_000002945.3_ASM294v3 fungi GCA_000003205.6_Btau_5.0.1 mammals GCA_000003525.2_BD_ER3_V1 fungi GCA_000003625.1_OryCun2.0 mammals GCA_000003835.1_ASM383v1 fungi GCA_000003855.2_BD_SLH14081_V1 fungi +GCA_000005575.1_AgamP3 invertebrate GCA_000005845.2_ASM584v2 bacteria GCA_000091045.1_ASM9104v1 fungi GCA_000146795.3_Nleu_3.0 primates GCA_000147415.1_v_1.0 plants GCA_000149205.2_ASM14920v2 fungi GCA_000149685.1_ASM14968v1 fungi GCA_000151335.1_JCVI-cpa1-1.0 fungi GCA_000151735.1_Cavpor3.0 mammals GCA_000165445.3_Mmur_3.0 primates GCA_000182895.1_CC3 fungi GCA_000184155.1_FraVesHawaii_1.0 plants +GCA_000208615.1_JCVI_ISG_i3_1.0 invertebrate GCA_000208655.2_Dasnov3.0 mammals +GCA_000209185.1_CulPip1.0 invertebrate GCA_000219625.1_MYCGR_v2.0 fungi GCA_000226395.1_PenChr_Nov2007 fungi GCA_000243295.1_TriManLat1.0 mammals GCA_000247695.1_HetGla_female_1.0 mammals GCA_000247795.2_Bos_indicus_1.0 mammals GCA_000258655.2_panpan1.1 primates GCA_000260255.1_OctDeg1.0 mammals GCA_000264685.2_Panu_3.0 primates GCA_000271745.2_FO_FOSC_3_a_V1 fungi GCA_000280705.1_JacJac1.0 mammals GCA_000283155.1_CerSimSim1.0 mammals GCA_000292845.1_OchPri3.0 mammals GCA_000295675.1_oxytricha_asm_v1.1 invertebrate GCA_000296755.1_EriEur2.0 mammals GCA_000311805.2_CB1 mammals GCA_000313985.1_EchTel2.0 mammals GCA_000315645.2_PdigPd1_v1 fungi GCA_000349665.1_MesAur1.0 mammals GCA_000349705.1_LepWed1.0 mammals GCA_000364345.1_Macaca_fascicularis_5.0 primates GCA_000365465.3_Ptep_3.0 invertebrate GCA_000371365.1_Musca_domestica-2.0.2 invertebrate GCA_000409795.2_Chlorocebus_sabeus_1.1 primates GCA_000442215.1_Lipotes_vexillifer_v1 mammals +GCA_000457365.2_ASM45736v2 invertebrate GCA_000464555.1_PanTig1.0 mammals GCA_000471725.1_UMD_CASPUR_WB_2.0 mammals GCA_000493695.1_BalAcu1.0 mammals +GCA_000499545.1_ETH001 invertebrate +GCA_000507465.4_ASM50746v4 fungi +GCA_000512565.3_ASM51256v3 fungi +GCA_000512585.3_ASM51258v3 fungi GCA_000622305.1_S.galili_v1.0 mammals GCA_000687225.1_UrsMar_1.0 mammals GCA_000696695.1_Burgud mammals GCA_000710875.1_Pepper_Zunla_1_Ref_v1.0 plants GCA_000741045.2_Vradiata_ver6 plants GCA_000750555.1_ASM75055v1 bacteria GCA_000754665.1_Bison_UMD1.0 mammals GCA_000767525.1_Vi_pacos_V1.0 mammals GCA_000767585.1_PRJNA234474_Ca_dromedarius_V1.0 mammals GCA_000767855.1_Ca_bactrianus_MBC_1.0 mammals GCA_000769185.1_Rrox_v1 primates GCA_000772875.3_Mmul_8.0.1 primates GCA_000845685.2_ViralProj14462 viral GCA_000952055.2_Anan_2.0 primates GCA_000956105.1_Pcoq_1.0 primates GCA_000961545.1_S_schenckii_v1 fungi GCA_000968595.1_ASM96859v1 fungi GCA_001015335.1_Stomoxys_calcitrans-1.0.1 invertebrate GCA_001189475.1_ASM118947v1 fungi GCA_001305755.1_ASM130575v1 mammals GCA_001417885.1_Kmar_1.0 fungi GCA_001417965.1_Aiptasia_genome_1.1 invertebrate GCA_001443585.1_aciJub1 mammals +GCA_001457755.2_Trypanosoma_equiperdum_OVI_V2 invertebrate GCA_001624215.1_A_J_v1 mammals GCA_001624295.1_AKR_J_v1 mammals GCA_001624475.1_CBA_J_v1 mammals GCA_001624505.1_DBA_2J_v1 mammals GCA_001624535.1_FVB_NJ_v1 mammals GCA_001624675.1_NOD_ShiLtJ_v1 mammals GCA_001624745.1_NZO_HlLtJ_v1 mammals GCA_001624775.1_PWK_PhJ_v1 mammals GCA_001624835.1_WSB_EiJ_v1 mammals GCA_001624865.1_SPRET_EiJ_v1 mammals GCA_001632525.1_BALB_cJ_v1 mammals GCA_001632575.1_C3H_HeJ_v1 mammals GCA_001632615.1_LP_J_v1 mammals GCA_001685135.1_ManJav1.0 mammals GCA_001698545.1_ASM169854v1 primates GCA_001704415.1_ARS1 mammals +GCA_001720195.2_ASM172019v2 fungi GCA_001857705.1_PanPar1.0 mammals GCA_001890085.1_ASM189008v1 mammals GCA_001922835.1_NIST_Tur_tru_v1 mammals GCA_002007445.1_ASM200744v1 mammals GCA_002007445.2_ASM200744v2 mammals GCA_002102435.1_Ovir.te_1.0 mammals GCA_002114115.1_ASM211411v1 plants GCA_002156985.1_Harm_1.0 invertebrate GCA_002201575.1_ASM220157v1 mammals GCA_002204515.1_AaegL5.0 invertebrate GCA_002288905.2_ASM228890v2 mammals GCA_002288925.2_ASM228892v2 mammals GCA_002754865.1_ASM275486v1 primates GCA_002775015.1_Cand_auris_B11221_V1 fungi GCA_002776525.1_ASM277652v1 primates @@ -126,30 +137,31 @@ GCA_004025105.1_TamTet_v1_BIUU mammals GCA_004026685.1_MonMon_M_v1_BIUU mammals GCA_004026725.1_OnyTor_v1_BIUU mammals GCA_004026785.1_MerUng_v1_BIUU mammals GCA_004026985.1_MyoMyo_v1_BIUU mammals GCA_004027225.2_bStrHab1.2.pri birds GCA_004027395.1_CanFam_VD_v1_BIUU mammals GCA_004027435.1_ArtJam_v1_BIUU mammals GCA_004027515.1_AntAmePen_v1_BIUU mammals GCA_004027675.1_CasCan_v1_BIUU mammals GCA_004027815.1_NycCou_v1_BIUU primates GCA_004027855.1_ChoDid_v1_BIUU mammals GCA_004027935.1_ChrAsi_v1_BIUU mammals GCA_004115215.3_mOrnAna1.pri.v3 mammals GCA_004115265.2_mRhiFer1_v1.p mammals +GCA_004337985.1_PpBr36 fungi GCA_004363495.1_PhoPho_v1_BIUU mammals GCA_004363515.1_IniGeo_v1_BIUU mammals GCA_004365145.1_OryAfe_v1_BIUU mammals GCA_004365275.1_TupTan_v1_BIUU mammals GCA_006229205.1_meerkat_22Aug2017_6uvM2_HiC mammals GCA_006496715.1_Aalbo_primary.1 invertebrate GCA_007210705.1_Tcal_SD_v2.1 invertebrate GCA_007364275.2_fArcCen1 fish GCA_009663435.1_Callithrix_jacchus_cj1700_1.0 primates GCA_009762305.1_mZalCal1.pri mammals GCA_009762595.1_rDerCor1.alt vertebrate GCA_009764475.1_sPriPec2.pri vertebrate GCA_009764565.1_rDerCor1.pri vertebrate GCA_009769485.1_bCygOlo1.alt birds GCA_009769545.1_fCycLum1.pri fish @@ -165,36 +177,38 @@ GCA_011004845.1_fEsoLuc1.pri fish GCA_011064685.1_ZJU_Sfru_1.0 invertebrate GCA_011100535.1_mCalJac1.pat primates GCA_011100555.2_mCalJa1.2.pat.X primates GCA_011100635.1_mTriVul1.pri mammals GCA_011762505.1_mArvNil1.pat.X mammals GCA_011762595.1_mTurTru1.mat.Y mammals GCA_012275295.1_bMelUnd1.mat.Z birds GCA_013339725.1_BIME_Rmic_1.3 invertebrate GCA_013347855.1_fAngAng1.pri vertebrate GCA_014108255.1_mRhiFer1.p mammals GCA_014176215.1_mRouAeg1.p mammals GCA_014356525.1_ASM1435652v1 invertebrate GCA_014839835.1_bDryPub1.pri birds GCA_014905235.2_Bmori_2016v1.0 invertebrate +GCA_015104395.1_ASM1510439v1 invertebrate GCA_015227675.2_mRatBN7.2 mammals GCA_015227805.2_bHirRus1.pri.v2 birds GCA_015227805.3_bHirRus1.pri.v3 birds GCA_016128335.1_ZJU1.0 birds GCA_016432865.1_AdamAnt mammals GCA_017916325.1_LU_Lmar_1.0 invertebrate +GCA_017916335.1_LU_Lori_1.0 invertebrate GCA_017976375.1_bCucCan1.pri birds GCA_017976425.1_fToxJac2.pri fish GCA_018139145.1_ASM1813914v1 birds GCA_018296145.1_Otsh_v2.0 fish GCA_018852605.1_HG002.alt.pat.f1_v2 primates GCA_018852615.1_HG002.pri.mat.f1_v2 primates GCA_019393635.1_mDroGli1.pri mammals GCA_019925205.1_ASM1992520v1 invertebrate GCA_020740725.1_bCorHaw1.pri.cur birds GCA_020740795.1_bApuApu2.pri.cur birds GCA_020745735.1_sHemOce1.pat.X.cur. vertebrate GCA_020826845.1_mDicBic1.mat.cur mammals GCA_021462225.2_DD_fGirMul_XY1 fish GCA_021950905.1_HG002.pat.cur.20211005 primates GCA_021951015.1_HG002.mat.cur.20211005 primates @@ -279,115 +293,128 @@ GCA_947179515.1_mApoSyl1.1 mammals GCA_947347685.1_fPlePla1.1 fish GCA_949774975.1_mLagAlb1.1 mammals GCA_949987515.1_mDelDel1.1 mammals GCA_949987535.1_mBalAcu1.1 mammals GCA_950005125.1_mChiNiv1.1 mammals GCA_950295315.1_mEriEur2.1 mammals GCA_958295425.1_fSolSol10.1 fish GCA_963082965.1_fCarCar2.1 fish GCA_963259705.1_mMyoDau2.1 mammals GCA_963514075.1_fConCon1.1 fish GCF_000001405.39_GRCh38.p13 primates GCF_000001405.40_GRCh38.p14 primates GCF_000001635.26_GRCm38.p6 mammals GCF_000001735.3_TAIR10 plants +GCF_000002435.1_GL2 invertebrate +GCF_000002435.2_UU_WB_2.1 invertebrate GCF_000002595.1_v3.0 plants GCF_000002775.4_Pop_tri_v3 plants GCF_000002855.3_ASM285v2 fungi GCF_000002945.1_ASM294v2 fungi +GCF_000002945.2_ASM294v3 fungi GCF_000002995.3_ASM299v2 invertebrate GCF_000004335.2_AilMel_1.0 mammals GCF_000004515.4_Glycine_max_v2.0 plants GCF_000004515.5_Glycine_max_v2.1 plants GCF_000004555.1_ASM455v1 invertebrate GCF_000004665.1_Callithrix_jacchus-3.2 primates +GCF_000005575.2_AgamP3 invertebrate GCF_000005975.2_dyak_caf1 invertebrate GCF_000006175.1_ASM617v2 archaea GCF_000090795.1_v1.0 invertebrate GCF_000091225.1_ASM9122v1 fungi GCF_000143185.1_v1.0 fungi GCF_000149645.2_ASM14964v3 fungi GCF_000164845.3_VicPac3.1 mammals GCF_000165045.1_Callorhinchus_milii-6.1.3 vertebrate GCF_000181695.1_ASM18169v1 fungi GCF_000182805.2_ASM18280v2 fungi GCF_000188115.4_SL3.0 plants GCF_000189315.1_Devil_ref_v7.0 mammals GCF_000203795.1_v1.0 fungi +GCF_000208615.1_JCVI_ISG_i3_1.0 invertebrate GCF_000208655.1_Dasnov3.0 mammals +GCF_000209185.1_CulPip1.0 invertebrate GCF_000215625.1_MusPutFur1.0 mammals GCF_000231095.1_Oryza_brachyantha.v1.4b plants GCF_000235385.1_SaiBol1.0 primates GCF_000236235.1_SpeTri2.0 mammals GCF_000241765.3_Chrysemys_picta_bellii-3.0.3 vertebrate GCF_000241765.4_Chrysemys_picta_BioNano-3.0.4 vertebrate GCF_000255335.1_Mocc_1.0 invertebrate GCF_000264685.3_Panu_3.0 primates GCF_000300575.1_Agabi_varbisH97_2 fungi GCF_000326865.1_Helobdella_robusta_v1.0 invertebrate GCF_000340665.1_C.cajan_V1.0 plants GCF_000341935.1_Ccin1 invertebrate GCF_000344595.1_CheMyd_1.0 vertebrate GCF_000364345.1_Macaca_fascicularis_5.0 primates GCF_000365465.2_Ptep_2.0 invertebrate GCF_000442215.1_Lipotes_vexillifer_v1 mammals +GCF_000457365.1_ASM45736v1 invertebrate GCF_000471905.2_AMTR1.0 plants GCF_000495115.1_PopEup_1.0 plants +GCF_000499545.1_ETH001 invertebrate GCF_000503995.1_CerSol_1.0 invertebrate GCF_000507465.1_Kwon_mang_CBS8507_V2 fungi +GCF_000507465.2_ASM50746v4 fungi GCF_000511025.2_RefBeet-1.2.2 plants GCF_000512565.1_Cryp_deje_CBS10117_V1 fungi +GCF_000512565.2_ASM51256v3 fungi GCF_000512585.1_Cryp_best_CBS10118_V1 fungi +GCF_000512585.2_ASM51258v3 fungi GCF_000687205.1_ASM68720v1 birds GCF_000690535.1_ASM69053v1 birds GCF_000691845.1_ASM69184v1 birds GCF_000695815.1_ASM69581v1 birds GCF_000697945.2_Focc_2.1 invertebrate GCF_000699005.1_ASM69900v1 birds GCF_000699245.1_ASM69924v1 birds GCF_000699445.2_SchHae_2.0 invertebrate GCF_000700745.1_ASM70074v1 birds GCF_000709325.1_ASM70932v1 birds GCF_000709365.1_ASM70936v1 birds GCF_000738735.2_ASM73873v2 birds GCF_000738735.5_ASM73873v5 birds GCF_000747805.1_ChaPel_1.0 birds GCF_000764305.1_Hazt_2.0 invertebrate GCF_000801105.1_Rs1.0 plants GCF_000806345.1_ASM80634v1 invertebrate GCF_000817695.2_Aradu1.1 plants GCF_000836235.1_Pxut_1.0 invertebrate GCF_000951615.1_common_carp_genome fish GCF_001194135.1_Octopus_bimaculoides_v2_0 invertebrate +GCF_001457755.1_Trypanosoma_equiperdum_OVI_V2 invertebrate GCF_001458135.1_marMar2.1 mammals GCF_001483705.1_ASM148370v1 invertebrate GCF_001531365.1_CcrdV1 plants GCF_001577835.1_Coturnix_japonica_2.0 birds GCF_001594065.1_Ccosl1.0 invertebrate GCF_001594075.1_Tcor1.0 invertebrate GCF_001633185.1_ValleyOak3.0 plants GCF_001640805.1_ASM164080v1 fish GCF_001649575.1_ASM164957v1 fish GCF_001652005.1_ASM165200v1 invertebrate GCF_001659605.1_Manihot_esculenta_v6 plants GCF_001660625.1_IpCoco_1.2 fish GCF_001660625.2_IpCoco_1.2 fish GCF_001663975.1_Xenopus_laevis_v2 vertebrate GCF_001687245.1_Rhagoletis_zephyria_1.0 invertebrate GCF_001698545.1_ASM169854v1 primates GCF_001704415.1_ARS1 mammals +GCF_001720195.1_ASM172019v2 fungi GCF_001890085.1_ASM189008v1 mammals GCF_001891065.1_H_comes_QL1_v1 fish GCF_002007445.1_ASM200744v2 mammals GCF_002021735.1_Okis_V1 fish GCF_002093755.1_Dser1.0 invertebrate GCF_002099425.1_phaCin_unsw_v4.1 mammals GCF_002162155.1_WEW_v2.0 plants GCF_002201575.1_ASM220157v1 mammals GCF_002263795.1_ARS-UCD1.2 mammals GCF_002263795.2_ARS-UCD1.3 mammals GCF_002443255.1_Vdes_3.0 invertebrate GCF_002532875.1_vjacob_1.0 invertebrate GCF_002571385.1_Stylophora_pistillata_v1 invertebrate GCF_002706865.1_ASM270686v1 invertebrate GCF_002776525.2_ASM277652v2 primates @@ -409,30 +436,31 @@ GCF_003668045.1_CriGri-PICR mammals GCF_003676075.1_ASM367607v1 mammals GCF_003676075.2_GSC_YBM_2.0 mammals GCF_003710045.1_USU_Nmel_1.2 invertebrate GCF_003945595.1_ASM394559v1 birds GCF_003957565.1_bTaeGut1_v1.p birds GCF_004011695.1_Arabiei_Me14 fungi GCF_004027225.1_bStrHab1_v1.p birds GCF_004115215.1_mOrnAna1.p.v1 mammals GCF_004115265.1_mRhiFer1_v1.p mammals GCF_004118075.1_ASM411807v1 plants GCF_004126475.1_mPhyDis1_v1.p mammals GCF_004153925.1_Obicornis_v3 invertebrate GCF_004193835.1_ASM419383v1 invertebrate GCF_004193835.2_ASM419383v2 invertebrate +GCF_004337985.1_PpBr36 fungi GCF_004382195.1_ASM438219v1 invertebrate GCF_004664715.1_Pero_0.1 mammals GCF_005281655.1_TAMU_Nfulva_1.0 invertebrate GCF_005508785.1_pea_aphid_22Mar2018_4r6ur invertebrate GCF_006149115.1_Oner_1.0 fish GCF_006496715.1_Aalbo_primary.1 invertebrate GCF_007474595.1_mLynCan4_v1.p mammals GCF_008315115.1_SLUC_FBN_1 fish GCF_008629635.1_Kwon_shan_CBS_12478_V1 fungi GCF_008831285.1_ASM883128v1 plants GCF_009650485.1_drosAlbom15112-1751.03v1 invertebrate GCF_009764565.2_rDerCor1.pri.v3 vertebrate GCF_009819885.1_bCatUst1.pri birds GCF_009828535.1_HMol primates GCF_009828535.2_HMol_V2 primates @@ -441,42 +469,44 @@ GCF_010614865.1_ASM1061486v1 invertebrate GCF_010645085.1_ASM1064508v1 vertebrate GCF_010909765.1_sAmbRad1.pri vertebrate GCF_011064685.1_ZJU_Sfru_1.0 invertebrate GCF_011947565.2_Ppol_2 invertebrate GCF_012460135.1_BPBGC_Mater_1.0 birds GCF_013339695.1_ASM1333969v1 invertebrate GCF_013339745.1_ASM1333974v1 invertebrate GCF_013377495.1_Cygnus_atratus_primary_v1.0 birds GCF_014356525.1_ASM1435652v1 invertebrate GCF_014805625.1_Yale_Gfus_2 invertebrate GCF_014824575.1_WHU_Shon_v2 mammals GCF_014898055.1_MPIMG_talOcc4 mammals GCF_014898055.2_MPIMG_talOcc4v2 mammals GCF_014905685.1_NemWhi1 fish +GCF_015104395.2_ASM1510439v2 invertebrate GCF_015227805.1_bHirRus1.pri.v2 birds GCF_015228065.1_NSTDA_Pmon_1 invertebrate GCF_015237465.1_rCheMyd1.pri vertebrate GCF_016086655.2_UVic_Lsal_1.1 invertebrate GCF_016699345.1_BCM_Sbol_2.0 primates GCF_016700215.1_bGalGal1.pat.whiteleghornlayer.GRCg7w birds GCF_016746245.1_Prin_Dsan_1.0 invertebrate GCF_016746365.1_Prin_Dyak_Tai18E2_2.0 invertebrate GCF_016746395.1_Prin_Dsim_3.0 invertebrate GCF_016801865.1_TS_Cpip_V1 invertebrate GCF_016920785.1_Ixodes_scapularus_ComboLowHiFi invertebrate GCF_017639655.1_bFalNau1.pat birds +GCF_017916335.1_LU_Lori_1.0 invertebrate GCF_021218885.1_Marmota_monax_Labrador192_V1.0 mammals GCF_021288785.1_ASM2128878v2 mammals GCF_022539665.1_CSIRO_AGI_Dcar_v0.2 invertebrate GCF_023065955.1_UrsArc1.0 mammals GCF_023343755.1_ASM2334375v1 fungi GCF_027563975.1_ilPloInte3.1 invertebrate GCF_028858775.1_NHGRI_mPanTro3-v1.1-hic.freeze_pri primates GCF_028878055.1_NHGRI_mSymSyn1-v1.1-hic.freeze_pri primates GCF_028878055.2_NHGRI_mSymSyn1-v2.0_pri primates GCF_028885625.1_NHGRI_mPonPyg2-v1.1-hic.freeze_pri primates GCF_028885655.1_NHGRI_mPonAbe1-v1.1-hic.freeze_pri primates GCF_029281585.1_NHGRI_mGorGor1-v1.1-0.2.freeze_pri primates GCF_029289425.1_NHGRI_mPanPan1-v1.1-0.1.freeze_pri primates GCF_900094665.1_CAROLI_EIJ_v1.1 mammals GCF_900246225.1_fAstCal1.2 fish