d7f16ed60951554dc44e4ef0833c92343e7077f4 hiram Fri Nov 17 15:10:04 2023 -0800 update to catch up some VGP assemblies refs #29545 diff --git src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt index 19dcf21..7e6d0f2 100644 --- src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt +++ src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt @@ -1,23 +1,24 @@ GCA_000001905.1_Loxafr3.0 mammals GCA_000002305.1_EquCab2.0 mammals GCA_000002595.3_Chlamydomonas_reinhardtii_v5.5 plants GCA_000002725.2_ASM272v2 invertebrate GCA_000002875.2_ASM287v2 invertebrate GCA_000003205.6_Btau_5.0.1 mammals GCA_000003525.2_BD_ER3_V1 fungi GCA_000003625.1_OryCun2.0 mammals +GCA_000005845.2_ASM584v2 bacteria GCA_000146795.3_Nleu_3.0 primates GCA_000147415.1_v_1.0 plants GCA_000151735.1_Cavpor3.0 mammals GCA_000165445.3_Mmur_3.0 primates GCA_000184155.1_FraVesHawaii_1.0 plants GCA_000208655.2_Dasnov3.0 mammals GCA_000219625.1_MYCGR_v2.0 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_000280705.1_JacJac1.0 mammals GCA_000283155.1_CerSimSim1.0 mammals @@ -110,95 +111,122 @@ GCA_009764475.1_sPriPec2.pri vertebrate GCA_009764565.1_rDerCor1.pri vertebrate GCA_009769485.1_bCygOlo1.alt birds GCA_009769545.1_fCycLum1.pri fish GCA_009769625.1_bCygOlo1.pri birds GCA_009806435.2_UM_NZW_1.0 mammals GCA_009819505.1_bCatUst1.alt birds GCA_009819705.1_fHipHip1.pri fish GCA_009829125.1_fPerMag1.pri fish GCA_009873245.2_mBalMus1.v2 mammals GCA_009914755.4_T2T-CHM13v2.0 primates GCA_010909765.1_sAmbRad1.pri vertebrate 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_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_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_017976375.1_bCucCan1.pri birds +GCA_017976425.1_fToxJac2.pri fish GCA_018139145.1_ASM1813914v1 birds GCA_018296145.1_Otsh_v2.0 fish GCA_020740725.1_bCorHaw1.pri.cur birds GCA_020740795.1_bApuApu2.pri.cur birds GCA_020826845.1_mDicBic1.mat.cur mammals -GCA_023634155.1_bFalPer1.pri birds +GCA_021462225.2_DD_fGirMul_XY1 fish +GCA_023343835.1_bLagMut1_primary birds GCA_023634085.1_bFalChe1.pri birds +GCA_023634155.1_bFalPer1.pri birds GCA_023638135.1_bFalBia1.pri birds GCA_025265405.1_mMesDen1_primary_haplotype mammals +GCA_026419915.1_bHarHar1_primary_haplotype birds GCA_026419965.1_mKogBre1_haplotype_1 mammals +GCA_027172205.1_rPodRaf1.pri vertebrate +GCA_027358585.1_fPanHyp1.pri fish +GCA_027406575.1_mNycCou1.pri mammals +GCA_027409825.1_fScoJap1.pri fish GCA_027477595.1_bHaeMex1.pri birds GCA_027579445.1_bAmmNel1.pri birds +GCA_027579735.1_aBomBom1.pri vertebrate GCA_027887145.1_bAmmCau1.pri birds +GCA_027887155.1_rMalTer1.hap1 vertebrate GCA_027887165.1_mMonDom1.pri mammals GCA_028018845.1_bMelGeo1.pri birds GCA_028023285.1_mBalRic1.hap2 mammals GCA_028500815.1_bRisTri1.patW.cur.20221130 birds +GCA_028858705.1_bGruAme1.mat birds +GCA_029499605.1_aHylSar1.hap1 vertebrate +GCA_029633865.1_fLamInc1.hap2 fish +GCA_030028045.1_mHipAmp2.hap2 mammals GCA_030144855.1_sHypSab1.hap1 vertebrate +GCA_030435805.1_mMusLut2.pri mammals +GCA_030684315.1_sSteTig4.hap1 vertebrate GCA_030867065.1_rAllMis1 vertebrate +GCA_030867095.1_rAllMis1 vertebrate GCA_030936135.1_bGavSte3.hap2 birds GCA_900006655.3_Susie3 primates GCA_900094665.2_CAROLI_EIJ_v1.1 mammals GCA_900324465.2_fAnaTes1.2 fish GCA_900634415.1_fCotGob3.1 fish GCA_900634775.1_fGouWil2.1 fish GCA_901343595.1_MONAX5 mammals GCA_901699155.1_bStrTur1.1 birds GCA_901699165.1_bStrTur1.1_alternate_haplotype birds GCA_901709675.1_fSynAcu1.1 fish GCA_902153765.1_bAquChr1.2_alternate_haplotype birds GCA_902459505.1_aGeoSer1.1 vertebrate GCA_902500255.1_fThaAma1.1 fish GCA_902686455.1_mSciVul1.1 mammals +GCA_902713425.2_fAciRut3.2_maternal_haplotype fish GCA_904849725.1_MorexV3_pseudomolecules_assembly plants GCA_905147045.1_ilAglIoxx1.1 invertebrate GCA_905147105.1_ilPieBrab1.1 invertebrate GCA_905147365.1_ilAriAges1.1 invertebrate GCA_905147765.2_ilVanAtal1.2 invertebrate GCA_905147795.1_ilPieRapa1.1 invertebrate GCA_905163445.1_ilParAegt1.1 invertebrate GCA_905220365.1_ilVanCard2.1 invertebrate GCA_905220415.1_ilColCroc2.1 invertebrate GCA_905220565.1_ilMelCinx1.1 invertebrate GCA_905237065.2_Ssal_v3.1 fish GCA_905333055.1_ilManJurt1.1 invertebrate GCA_905404315.1_ilLepSina1.1 invertebrate GCA_905475465.1_ilPieNapi1.1 invertebrate +GCA_910596095.1_fThuMac1.1 fish 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 GCF_000001405.39_GRCh38.p13 primates GCF_000001405.40_GRCh38.p14 primates GCF_000001635.26_GRCm38.p6 mammals GCF_000001735.3_TAIR10 plants GCF_000002595.1_v3.0 plants GCF_000002775.4_Pop_tri_v3 plants GCF_000002855.3_ASM285v2 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_000005975.2_dyak_caf1 invertebrate GCF_000006175.1_ASM617v2 archaea @@ -287,30 +315,31 @@ GCF_002870075.2_Lsat_Salinas_v7 plants GCF_002870075.3_Lsat_Salinas_v8 plants GCF_002906115.1_CorkOak1.0 plants GCF_002922805.1_Om_v0.7.RACA fish GCF_002940915.1_ASM294091v2 mammals GCF_002994745.1_RchiOBHm-V2 plants GCF_003031525.1_Neophocaena_asiaeorientalis_V1 mammals GCF_003227715.1_Hsal_v8.5 invertebrate GCF_003584765.1_ASM358476v1 mammals 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_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_007474595.1_mLynCan4_v1.p mammals GCF_008315115.1_SLUC_FBN_1 fish @@ -356,19 +385,19 @@ GCF_900324485.1_fMasArm1.1 fish GCF_900496995.1_bAquChr1.2 birds GCF_900634625.1_fParRan2.1 fish GCF_900634775.1_fGouWil2.1 fish GCF_900634795.2_fBetSpl5.2 fish GCF_900634795.3_fBetSpl5.3 fish GCF_900700375.1_fDenClu1.1 fish GCF_900700415.1_Ch_v2.0.2 fish GCF_900747795.1_fErpCal1.1 vertebrate GCF_900880675.1_fSpaAur1.1 fish GCF_900963305.1_fEcheNa1.1 fish GCF_901001135.1_aRhiBiv1.1 vertebrate GCF_901001165.1_fSalTru1.1 fish GCF_902150015.1_genome_assembly_l500 birds GCF_902459505.1_aGeoSer1.1 vertebrate +GCF_902713615.1_sScyCan1.1 vertebrate GCF_903992535.1_mArvAmp1.1 mammals GCF_922984935.1_mMelMel3.1_paternal_haplotype mammals GCF_932274485.1_xgPatVulg1.1 invertebrate -GCF_902713615.1_sScyCan1.1 vertebrate