Multiz 470-way Track Settings
Multiz Alignment & Conservation (470 mammals)   (All Comparative Genomics tracks)

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Multiz Alignments ▾       Basewise Conservation (phyloP) ▾       Element Conservation (phastCons) ▾       Conserved Elements ▾      
Multiz Alignments Configuration

Species selection:  + - default

  Primates  + -

northern white-cheeked gibbon
silvery gibbon
crab-eating macaque
Japanese macaque
golden snub-nosed monkey
green monkey
olive baboon
sooty mangabey
pig-tailed macaque
Francois's langur
Red shanked douc langur
Ugandan red Colobus
red guenon
Allen's swamp monkey
black snub-nosed monkey
Mona monkey
Hanuman langur
angolan colobus
De Brazza's monkey
white-faced saki
black-handed spider monkey
tufted capuchin
mantled howler monkey
Bolivian titi
white-faced sapajou
white-tufted-ear marmoset
ma's night monkey
pygmy marmoset
white-fronted capuchin
proboscis monkey
Bolivian squirrel monkey
squirrel monkey
Northern giant mouse lemur
black lemur
mouse lemur
greater bamboo lemur
Sclater's lemur
Coquerel's mouse lemur
Ring-tailed lemur
Lesser dwarf lemur
mouse lemur
brown lemur
sclater's lemur
Northern rufous mouse lemur
mongoose lemur
coquerel's sifaka
slow loris

  Euarchontoglires  + -

Sunda flying lemur
chinese tree shrew
tree shrew

  Carnivore  + -

harbor seal
California sea lion
grizzly bear
Steller sea lion
pacific walrus
hawaiian monk seal
northern fur seal
Southern elephant seal
Asian black bear
bearded seal
gray seal
Northern elephant seal
American black bear
giant panda
Clouded leopard
American black bear
Canada lynx
weddell seal
antarctic fur seal
Spanish lynx
Amur leopard cat
lesser panda
Northern American river otter
Eurasian river otter
red fox
giant otter
African hunting dog
striped hyena
southern sea otter
giant otter
black-footed cat
domestic ferret
Arctic fox
European polecat
spotted hyena
Asian palm civet
American mink
banded mongoose
western spotted skunk
dwarf mongoose
North American badger
White-nosed coati
African hunting dog

  Laurasiatheria  + -

black rhinoceros
white rhinoceros
greater Indian rhinoceros
Sumatran rhinoceros
Asiatic tapir
Brazilian tapir
Asiatic tapir
northern white rhinoceros
Equus burchelli boehmi
Chinese pangolin
Tree pangolin
Malayan pangolin
Malayan pangolin
Tree pangolin
chinese pangolin
Hispaniolan solenodon
Iberian mole
eastern mole
gracile shrew mole
star-nosed mole

  Cetartiodactyla  + -

grey whale
sperm whale
beluga whale
common bottlenose dolphin
Indo-pacific bottlenose dolphin
killer whale
Indo-pacific humpbacked dolphin
Indo-pacific bottlenose dolphin
Antarctic minke whale
harbor porpoise
harbor porpoise
common bottlenose dolphin
Arabian camel
Wild Bactrian camel
Bactrian camel
water buffalo
white-tailed deer
Pere David's deer
zebu cattle
white-tailed deer
wild yak
wild goat
tibetan antelope
Masai giraffe
bighorn sheep
greater kudu

  Artiodactyla  + -

Blue whale
North Atlantic right whale
pygmy Bryde's whale
minke whale
North Pacific right whale
humpback whale
Pacific white-sided dolphin
long-finned pilot whale
melon-headed whale
bowhead whale
Yangtze finless porpoise
Indus River dolphin
Fin whale
Sowerby's beaked whale
pygmy sperm whale
Vicugna mensalis
Lama pacos huacaya
Cuvier's beaked whale
Yarkand deer
Hog deer
porcupine caribou
Asiatic mouflon
African buffalo
scimitar-horned oryx
Siberian ibex
Reeves' muntjac
Chacoan peccary
roan antelope
sable antelope
Eastern roe deer
Chinese water deer
white-tailed deer
white-lipped deer
Nilgiri tahr
Siberian musk deer
Cobus hunteri
Eurasian elk
snow sheep
brindled gnu
mule deer
Thomson's gazelle
mountain goat
domestic yak
Chinese forest musk deer
Harvey's duiker
bighorn sheep
black muntjac
Przewalski's gazelle
Kirk's dik-dik
bush duiker
Java mouse-deer
Bohar reedbuck
saiga antelope
Central European red deer
Grant's gazelle
lesser kudu
royal antelope
Maxwell's duiker
lesser mouse-deer
alpine musk deer
Alpine ibex

  Xenarthra  + -

southern two-toed sloth
Hoffmann's two-fingered sloth
southern two-toed sloth
southern tamandua
giant anteater
Southern three-banded armadillo

  Chiroptera  + -

greater horseshoe bat
Chinese rufous horseshoe bat
Bonin flying fox
Indian flying fox
black flying-fox
Malagasy flying fox
Cantor's roundleaf bat
Egyptian rousette
large flying fox
Leschenault's rousette
great roundleaf bat
lesser dawn bat
Malagasy straw-colored fruit bat
long-tongued fruit bat
straw-colored fruit bat
Brazilian free-tailed bat
Madagascan rousette
common vampire bat
Pallas's mastiff bat
pale spear-nosed bat
Lesser long-nosed bat
Antillean ghost-faced bat
Indian false vampire
stripe-headed round-eared bat
tailed tailless bat
Seba's short-tailed bat
Jamaican fruit-eating bat
Miniopterus schreibersii natalensis
Jamaican fruit-eating bat
Schreibers' long-fingered bat
California big-eared bat
Honduran yellow-shouldered bat
lesser short-nosed fruit bat
greater mouse-eared bat
Schizostoma hirsutum
hog-nosed bat
Northern long-eared myotis
big brown bat
little brown bat
little brown bat
greater bulldog bat
david's myotis (bat)
Murina feae
evening bat
pallid bat
hoary bat
red bat
Kuhl's pipistrelle
common pipistrelle
common pipistrelle

  Glires  + -

gray squirrel
Eurasian red squirrel
yellow-bellied marmot
South African ground squirrel
Alpine marmot
Gunnison's prairie dog
Himalayan marmot
Daurian ground squirrel
Vancouver Island marmot
Arctic ground squirrel
North American porcupine
mountain beaver
Fat dormouse
naked mole-rat
crested porcupine
Brazilian porcupine
punctate agouti
American beaver
European rabbit
woodland dormouse
Damara mole-rat
snowshoe hare
brush rabbit
Montane guinea pig
Patagonian cavy
guinea pig
hazel dormouse
Mountain hare
brush-tailed rat
northern gundi
social tuco-tuco
Greater cane rat
Peromyscus californicus subsp. insignis
Hesperomys crinitus
prairie deer mouse
oldfield mouse
northern rock mouse
white-footed mouse
cactus mouse
hoary bamboo rat
southern grasshopper mouse
Gobi jerboa
lesser Egyptian jerboa
Gambian giant pouched rat
Chinese hamster
African woodland thicket rat
Eurasian water vole
African grass rat
Northern mole vole
Stephens's kangaroo rat
golden spiny mouse
southern multimammate mouse
meadow jumping mouse
short-tailed field vole
fat sand rat
western wild mouse
Bank vole
Ryukyu mouse
prairie vole
Norway rat
Transcaucasian mole vole
shrew mouse
great gerbil
Egyptian spiny mouse
steppe mouse
reed vole
Common vole
root vole
hispid cotton rat
black rat
desert woodrat
golden hamster
Mongolian gerbil
Pacific pocket mouse
European woodmouse

  Afrotheria  + -

African savanna elephant
Asiatic elephant
Cape rock hyrax
yellow-spotted hyrax
cape golden mole
Steller's sea cow
cape elephant shrew
Talazac's shrew tenrec

  Metatheria  + -

common wombat
common brushtail
Leadbeater's possum
eastern gray kangaroo
ground cuscus
tammar wallaby
yellow-footed antechinus
western gray kangaroo
Tasmanian devil
coppery ringtail possum
Agile Gracile Mouse Opossum
red kangaroo
North American opossum
golden ringtail possum
Western ringtail oppossum
Tasmanian wolf

  Monotremata  + -

Australian echidna

Multiple alignment base-level:
Display bases identical to reference as dots
Display chains between alignments

Codon Translation:
Default species to establish reading frame:
No codon translation
Use default species reading frames for translation
Use reading frames for species if available, otherwise no translation
Use reading frames for species if available, otherwise use default species
List subtracks: only selected/visible    all  
 470 phyloP  470 mammals Basewise Conservation by PhyloP   Data format 
 Multiz 470-way  Multiz Alignments of 470 mammals   Data format 
 Cons 470 Mammals  470 mammals conservation by PhastCons   Data format 
 470 Mamm. El  470 mammals Conserved Elements   Data format 
Assembly: Human Dec. 2013 (GRCh38/hg38)

Data Access

Downloads for data in this track are available:


This track shows multiple alignments of 470 mammal assemblies and measurements of evolutionary conservation from the Michael Hiller Lab. There is some duplication of different assemblies for the same species, hence there are 431 distinct species in this collection.

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 base-wise conservation scores are computed using two methods phastCons and phyloP from the PHAST package, for all species.

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).

The genome assemblies are from a variety of sources. Some are equivalent to UCSC genome browser assemblies, some are from NCBI Genbank assemblies, and some are from the DNA Zoo. When available in the UCSC browser system, links are provided in the table below. Otherwise, links are provided to source locations for the assemblies.

count common
clade scientific
link to browser when available, or assembly source
taxon id
link to NCBI
1 human primates Homo sapiens Dec. 2013 (GRCh38/hg38) 9606
2 chimpanzee Primates Pan troglodytes Jan. 2018 (Clint_PTRv2/panTro6) 9598
3 pygmy chimpanzee Primates Pan paniscus May 2020 (Mhudiblu_PPA_v0/panPan3) 9597
4 western lowland gorilla Primates Gorilla gorilla gorilla Aug. 2019 (Kamilah_GGO_v0/gorGor6) 9595
5 Sumatran orangutan Primates Pongo abelii Jan. 2018 (Susie_PABv2/ponAbe3) 9601
6 northern white-cheeked gibbon Primates Nomascus leucogenys HLnomLeu4 GCA_006542625.1 61853
7 silvery gibbon Primates Hylobates moloch HLhylMol2 GCA_009828535.2 81572
8 pig-tailed macaque Primates Macaca nemestrina Mar. 2015 (Mnem_1.0/macNem1) 9545
9 gelada Primates Theropithecus gelada HLtheGel1 GCA_003255815.1 9565
10 crab-eating macaque Primates Macaca fascicularis HLmacFas6 GCA_012559485.1 9541
11 Mona monkey Primates Cercopithecus mona HLcerMon1 GCA_014849445.1 36226
12 Ugandan red Colobus Primates Piliocolobus tephrosceles HLpilTep2 GCA_002776525.3 591936
13 Angolan colobus Primates Colobus angolensis palliatus Mar. 2015 (Cang.pa_1.0/colAng1) 336983
14 drill Primates Mandrillus leucophaeus Mar. 2015 (Mleu.le_1.0/manLeu1) 9568
15 sooty mangabey Primates Cercocebus atys Mar. 2015 (Caty_1.0/cerAty1) 9531
16 olive baboon Primates Papio anubis HLpapAnu5 GCA_008728515.1 9555
17 mandrill Primates Mandrillus sphinx HLmanSph1 GCA_004802615.1 9561
18 Hanuman langur Primates Semnopithecus entellus HLsemEnt1 GCA_004025065.1_SemEnt_v1_BIUU 88029
19 Rhesus monkey Primates Macaca mulatta Feb. 2019 (Mmul_10/rheMac10) 9544
20 Japanese macaque Primates Macaca fuscata DNA zoo Macaca fuscata 9542
21 Francois's langur Primates Trachypithecus francoisi HLtraFra1 GCA_009764315.1 54180
22 black snub-nosed monkey Primates Rhinopithecus bieti Aug. 2016 (ASM169854v1/rhiBie1) 61621
23 golden snub-nosed monkey Primates Rhinopithecus roxellana HLrhiRox2 GCA_007565055.1 61622
24 Red shanked douc langur Primates Pygathrix nemaeus HLpygNem1 GCA_004024825.1_PygNem_v1_BIUU 54133
25 De Brazza's monkey Primates Cercopithecus neglectus HLcerNeg1 GCA_004027615.1_CertNeg_v1_BIUU 36227
26 proboscis monkey Primates Nasalis larvatus Nov. 2014 (Charlie1.0/nasLar1) 43780
27 Allen's swamp monkey Primates Allenopithecus nigroviridis DNA zoo Allenopithecus nigroviridis 54135
28 green monkey Primates Chlorocebus sabaeus Mar. 2014 (Chlorocebus_sabeus 1.1/chlSab2) 60711
29 red guenon Primates Erythrocebus patas HLeryPat1 GCA_004027335.1_EryPat_v1_BIUU 9538
30 white-faced saki Primates Pithecia pithecia HLpitPit1 GCA_004026645.1_PitPit_v1_BIUU 43777
31 black-handed spider monkey Primates Ateles geoffroyi HLateGeo1 GCA_004024785.1_AteGeo_v1_BIUU 9509
32 Ma's night monkey Primates Aotus nancymaae Jun. 2017 (Anan_2.0/aotNan1) 37293
33 Bolivian titi Primates Plecturocebus donacophilus HLpleDon1 GCA_004027715.1_CalDon_v1_BIUU 230833
34 mantled howler monkey Primates Alouatta palliata HLaloPal1 GCA_004027835.1_AloPal_v1_BIUU 30589
35 Bolivian squirrel monkey Primates Saimiri boliviensis DNA zoo Saimiri boliviensis 27679
36 tamarin Primates Saguinus imperator HLsagImp1 GCA_004024885.1_SagImp_v1_BIUU 9491
37 Bolivian squirrel monkey Primates Saimiri boliviensis boliviensis Oct. 2011 (Broad/saiBol1) 39432
38 white-tufted-ear marmoset Primates Callithrix jacchus HLcalJac4 GCA_011100555.1_mCalJac1.pat.X 9483
39 pygmy marmoset Primates Callithrix pygmaea DNA zoo Callithrix pygmaea 9493
40 tufted capuchin Primates Sapajus apella HLsapApe1 GCA_009761245.1 9515
41 Panamanian white-faced capuchin Primates Cebus capucinus imitator Apr. 2016 (Cebus_imitator-1.0/cebCap1) 2715852
42 white-fronted capuchin Primates Cebus albifrons HLcebAlb1 GCA_004027755.1_CebAlb_v1_BIUU 9514
43 aye-aye Primates Daubentonia madagascariensis HLdauMad1 GCA_004027145.1_DauMad_v1_BIUU 31869
44 Coquerel's sifaka Primates Propithecus coquereli Mar. 2015 (Pcoq_1.0/proCoq1) 379532
45 babakoto Primates Indri indri HLindInd1 GCA_004363605.1_IndInd_v1_BIUU 34827
46 brown lemur Primates Eulemur fulvus HLeulFul1 GCA_004027275.1_EulFul_v1_BIUU 13515
47 Sclater's lemur Primates Eulemur flavifrons Aug. 2015 (Eflavifronsk33QCA/eulFla1) 87288
48 Ring-tailed lemur Primates Lemur catta HLlemCat1 GCA_004024665.1_LemCat_v1_BIUU 9447
49 greater bamboo lemur Primates Prolemur simus HLproSim1 GCA_003258685.1 1328070
50 mongoose lemur Primates Eulemur mongoz DNA zoo Eulemur mongoz 34828
51 Sclater's lemur Primates Eulemur flavifrons DNA zoo Eulemur flavifrons 87288
52 Lesser dwarf lemur Primates Cheirogaleus medius HLcheMed1 GCA_008086735.1 9460
53 black lemur Primates Eulemur macaco Aug. 2015 (Emacaco_refEf_BWA_oneround/eulMac1) 30602
54 Philippine tarsier Primates Carlito syrichta Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2) 1868482
55 gray mouse lemur Primates Microcebus murinus Feb. 2017 (Mmur_3.0/micMur3) 30608
56 Northern giant mouse lemur Primates Mirza zaza HLmirZaz1 GCA_008750895.1 339999
57 Coquerel's mouse lemur Primates Mirza coquereli HLmirCoq1 GCA_004024645.1_MizCoq_v1_BIUU 47180
58 mouse lemur Primates Microcebus sp. 3 GT-2019 HLmicSpe31 GCA_008750915.1 2508170
59 Northern rufous mouse lemur Primates Microcebus tavaratra HLmicTav1 GCA_008750935.1 143351
60 slow loris Primates Nycticebus coucang HLnycCou1 GCA_004027815.1_NycCou_v1_BIUU 9470
61 small-eared galago Primates Otolemur garnettii Mar. 2011 (Broad/otoGar3) 30611
62 Sunda flying lemur Euarchontoglires Galeopterus variegatus HLgalVar2 GCA_004027255.2 482537
63 Chinese tree shrew Euarchontoglires Tupaia chinensis Jan 2013 (TupChi_1.0/tupChi1) 246437
64 northern tree shrew Euarchontoglires Tupaia belangeri Dec. 2006 (Broad/tupBel1) 37347
65 puma Carnivora Puma concolor HLpumCon1 GCA_003327715.1_PumCon1.0 9696
66 Amur tiger Carnivora Panthera tigris altaica 06 Sep 2013 (PanTig1.0/panTig1) 74533
67 Clouded leopard Carnivora Neofelis nebulosa DNA zoo Neofelis nebulosa 61452
68 leopard Carnivora Panthera pardus HLpanPar1 GCA_001857705.1_PanPar1.0 9691
69 bearded seal Carnivora Erignathus barbatus DNA zoo Erignathus barbatus 39304
70 jaguar Carnivora Panthera onca HLpanOnc1 GCA_004023805.1_PanOnc_v1_BIUU 9690
71 harbor seal Carnivora Phoca vitulina HLphoVit1 GCA_004348235.1 9720
72 cheetah Carnivora Acinonyx jubatus HLaciJub2 GCF_003709585.1_Aci_jub_2 32536
73 gray seal Carnivora Halichoerus grypus HLhalGry1 GCA_012393455.1 9711
74 Hawaiian monk seal Carnivora Neomonachus schauinslandi Jun. 2017 (ASM220157v1/neoSch1) 29088
75 Weddell seal Carnivora Leptonychotes weddellii Mar 2013 (LepWed1.0/lepWed1) 9713
76 jaguar Carnivora Panthera onca DNA zoo Panthera onca 9690
77 Amur leopard cat Carnivora Prionailurus bengalensis euptilurus HLpriBen1 GCA_005406085.1 300877
78 Asian black bear Carnivora Ursus thibetanus thibetanus HLursThi1 GCA_009660055.1 441215
79 Spanish lynx Carnivora Lynx pardinus HLlynPar1 GCA_900661375.1 191816
80 Southern elephant seal Carnivora Mirounga leonina HLmirLeo1 GCA_011800145.1 9715
81 Canada lynx Carnivora Lynx canadensis HLlynCan1 GCA_007474595.1 61383
82 Northern elephant seal Carnivora Mirounga angustirostris DNA zoo Mirounga angustirostris 9716
83 lion Carnivora Panthera leo HLpanLeo1 GCA_008795835.1 9689
84 walrus Carnivora Odobenus rosmarus DNA zoo Odobenus rosmarus 9707
85 northern fur seal Carnivora Callorhinus ursinus HLcalUrs1 GCA_003265705.1 34884
86 Pacific walrus Carnivora Odobenus rosmarus divergens Jan 2013 (Oros_1.0/odoRosDiv1) 9708
87 giant panda Carnivora Ailuropoda melanoleuca HLailMel2 GCA_002007445.2 9646
88 California sea lion Carnivora Zalophus californianus HLzalCal1 GCA_009762305.1_mZalCal1.pri 9704
89 Steller sea lion Carnivora Eumetopias jubatus HLeumJub1 GCA_004028035.1 34886
90 domestic cat Carnivora Felis catus Nov. 2017 (Felis_catus_9.0/felCat9) 9685
91 jaguarundi Carnivora Puma yagouaroundi HLpumYag1 GCA_014898765.1 1608482
92 grizzly bear Carnivora Ursus arctos horribilis HLursArc1 GCA_003584765.1 116960
93 polar bear Carnivora Ursus maritimus 09 May-2014 (UrsMar_1.0/ursMar1) 29073
94 antarctic fur seal Carnivora Arctocephalus gazella HLarcGaz2 GCA_900642305.1 37190
95 American black bear Carnivora Ursus americanus HLursAme1 GCA_003344425.1 9643
96 American black bear Carnivora Ursus americanus DNA zoo Ursus americanus 9643
97 black-footed cat Carnivora Felis nigripes HLfelNig1 GCA_004023925.1_FelNig_v1_BIUU 61379
98 fossa Carnivora Cryptoprocta ferox DNA zoo Cryptoprocta ferox 94188
99 red fox Carnivora Vulpes vulpes HLvulVul1 GCA_003160815.1 9627
100 dog Carnivora Canis lupus familiaris Mar. 2020 (UU_Cfam_GSD_1.0/canFam4) 9615
101 Arctic fox Carnivora Vulpes lagopus HLvulLag1 GCA_004023825.1_VulLag_v1_BIUU 494514
102 African hunting dog Carnivora Lycaon pictus DNA zoo Lycaon pictus 9622
103 dingo Carnivora Canis lupus dingo HLcanLupDin1 GCA_003254725.1 286419
104 dog Carnivora Canis lupus familiaris May 2019 (UMICH_Zoey_3.1/canFam5) 9615
105 kinkajou Carnivora Potos flavus DNA zoo Potos flavus 29067
106 African hunting dog Carnivora Lycaon pictus HLlycPic2 GCA_004216515.1 9622
107 lesser panda Carnivora Ailurus fulgens DNA zoo Ailurus fulgens 9649
108 spotted hyena Carnivora Crocuta crocuta HLcroCro1 GCA_008692635.1 9678
109 striped hyena Carnivora Hyaena hyaena HLhyaHya1 GCA_003009895.1 95912
110 Asian palm civet Carnivora Paradoxurus hermaphroditus HLparHer1 GCA_004024585.1_ParHer_v1_BIUU 71117
111 White-nosed coati Carnivora Nasua narica DNA zoo Nasua narica 352831
112 sable Carnivora Martes zibellina HLmarZib1 GCA_012583365.1 36722
113 wolverine Carnivora Gulo gulo HLgulGul1 GCA_900006375.2 48420
114 raccoon Carnivora Procyon lotor DNA zoo Procyon lotor 9654
115 Cacomistle Carnivora Bassariscus sumichrasti DNA zoo Bassariscus sumichrasti 392507
116 western spotted skunk Carnivora Spilogale gracilis HLspiGra1 GCA_004023965.1_SpiGra_v1_BIUU 30551
117 North American badger Carnivora Taxidea taxus jeffersonii HLtaxTax1 GCA_003697995.1 2282171
118 ratel Carnivora Mellivora capensis HLmelCap1 GCA_004024625.1_MelCap_v1_BIUU 9664
119 meerkat Carnivora Suricata suricatta HLsurSur2 GCA_004023905.1_SurSur_v1_BIUU 37032
120 meerkat Carnivora Suricata suricatta HLsurSur1 GCA_006229205.1 37032
121 banded mongoose Carnivora Mungos mungo HLmunMug1 GCA_004023785.1_MunMun_v1_BIUU 210652
122 dwarf mongoose Carnivora Helogale parvula HLhelPar1 GCA_004023845.1_HelPar_v1_BIUU 210647
123 Northern American river otter Carnivora Lontra canadensis HLlonCan1 GCA_010015895.1 76717
124 giant otter Carnivora Pteronura brasiliensis DNA zoo Pteronura brasiliensis 9672
125 giant otter Carnivora Pteronura brasiliensis HLpteBra1 GCA_004024605.1_PteBra_v1_BIUU 9672
126 Southern sea otter Carnivora Enhydra lutris nereis Jun. 2019 (ASM641071v1/enhLutNer1) 1049777
127 Northern sea otter Carnivora Enhydra lutris kenyoni Sep. 2017 (ASM228890v2/enhLutKen1) 391180
128 Eurasian river otter Carnivora Lutra lutra HLlutLut1 GCA_902655055.1 9657
129 ermine Carnivora Mustela erminea HLmusErm1 GCA_009829155.1 36723
130 American mink Carnivora Neovison vison HLneoVis1 GCA_900108605.1_NNQGG.v01 452646
131 European polecat Carnivora Mustela putorius HLmusPut1 GCA_902460205.1 9668
132 domestic ferret Carnivora Mustela putorius furo HLmusFur2 GCA_011764305.1 9669
133 Brazilian tapir Laurasiatheria Tapirus terrestris HLtapTer1 GCA_004025025.1_TapTer_v1_BIUU 9801
134 greater Indian rhinoceros Laurasiatheria Rhinoceros unicornis DNA zoo Rhinoceros unicornis 9809
135 Asiatic tapir Laurasiatheria Tapirus indicus HLtapInd1 GCA_004024905.1_TapInd_v1_BIUU 9802
136 Asiatic tapir Laurasiatheria Tapirus indicus DNA zoo Tapirus indicus 9802
137 black rhinoceros Laurasiatheria Diceros bicornis HLdicBic1 GCA_004027315.2 9805
138 Sumatran rhinoceros Laurasiatheria Dicerorhinus sumatrensis sumatrensis HLdicSum1 GCA_002844835.1_ASM284483v1 310712
139 northern white rhinoceros Laurasiatheria Ceratotherium simum cottoni HLcerSimCot1 GCA_004027795.1_CerCot_v1_BIUU 310713
140 southern white rhinoceros Laurasiatheria Ceratotherium simum simum May 2012 (CerSimSim1.0/cerSim1) 73337
141 Equus burchelli boehmi Laurasiatheria Equus burchellii boehmi DNA zoo Equus burchellii boehmi 89250
142 horse Laurasiatheria Equus caballus Jan. 2018 (EquCab3.0/equCab3) 9796
143 Przewalski's horse Laurasiatheria Equus przewalskii Jun 2014 (Burgud/equPrz1) 9798
144 ass Laurasiatheria Equus asinus HLequAsi1 GCA_001305755.1_ASM130575v1 9793
145 donkey Laurasiatheria Equus asinus asinus HLequAsiAsi2 GCA_003033725.1 83772
146 Tree pangolin Laurasiatheria Manis tricuspis HLmanTri1 GCA_004765945.1 358128
147 Tree pangolin Laurasiatheria Manis tricuspis DNA zoo Manis tricuspis 358128
148 Chinese pangolin Laurasiatheria Manis pentadactyla HLmanPen2 GCA_014570555.1 143292
149 Chinese pangolin Laurasiatheria Manis pentadactyla Aug 2014 (M_pentadactyla-1.1.1/manPen1) 143292
150 Malayan pangolin Laurasiatheria Manis javanica HLmanJav1 GCA_001685135.1_ManJav1.0 9974
151 Malayan pangolin Laurasiatheria Manis javanica HLmanJav2 GCA_014570535.1 9974
152 Hispaniolan solenodon Laurasiatheria Solenodon paradoxus HLsolPar1 GCA_004363575.1_SolPar_v1_BIUU 79805
153 eastern mole Laurasiatheria Scalopus aquaticus HLscaAqu1 GCA_004024925.1_ScaAqu_v1_BIUU 71119
154 Iberian mole Laurasiatheria Talpa occidentalis HLtalOcc1 GCA_014898055.1 50954
155 gracile shrew mole Laurasiatheria Uropsilus gracilis HLuroGra1 GCA_004024945.1_UroGra_v1_BIUU 182669
156 star-nosed mole Laurasiatheria Condylura cristata Mar 2012 (ConCri1.0/conCri1) 143302
157 western European hedgehog Laurasiatheria Erinaceus europaeus May 2012 (EriEur2.0/eriEur2) 9365
158 European shrew Laurasiatheria Sorex araneus Aug. 2008 (Broad/sorAra2) 42254
159 Antarctic minke whale Cetartiodactyla Balaenoptera bonaerensis HLbalBon1 GCA_000978805.1_ASM97880v1 33556
160 grey whale Cetartiodactyla Eschrichtius robustus HLescRob1 GCA_004363415.1_EscRob_v1_BIUU 9764
161 sperm whale Cetartiodactyla Physeter catodon Sep. 2013 (Physeter_macrocephalus-2.0.2/phyCat1) 9755
162 sperm whale Cetartiodactyla Physeter catodon HLphyCat2 GCA_002837175.2 9755
163 Yangtze River dolphin Cetartiodactyla Lipotes vexillifer 31 Jul 2013 (Lipotes_vexillifer_v1/lipVex1) 118797
164 beluga whale Cetartiodactyla Delphinapterus leucas HLdelLeu2 GCA_002288925.3 9749
165 hippopotamus Cetartiodactyla Hippopotamus amphibius HLhipAmp3 GCA_004027065.2 9833
166 hippopotamus Cetartiodactyla Hippopotamus amphibius HLhipAmp1 GCA_002995585.1_ASM299558v1 9833
167 harbor porpoise Cetartiodactyla Phocoena phocoena DNA zoo Phocoena phocoena 9742
168 harbor porpoise Cetartiodactyla Phocoena phocoena HLphoPho1 GCA_004363495.1_PhoPho_v1_BIUU 9742
169 Wild Bactrian camel Cetartiodactyla Camelus ferus HLcamFer3 GCA_009834535.1 419612
170 killer whale Cetartiodactyla Orcinus orca Jan. 2013 (Oorc_1.1/orcOrc1) 9733
171 Bactrian camel Cetartiodactyla Camelus bactrianus HLcamBac1 GCA_000767855.1_Ca_bactrianus_MBC_1.0 9837
172 Indo-pacific humpbacked dolphin Cetartiodactyla Sousa chinensis HLsouChi1 GCA_007760645.1 103600
173 Arabian camel Cetartiodactyla Camelus dromedarius HLcamDro2 GCA_000803125.3 9838
174 alpaca Cetartiodactyla Vicugna pacos Mar. 2013 (Vicugna_pacos-2.0.1/vicPac2) 30538
175 common bottlenose dolphin Cetartiodactyla Tursiops truncatus HLturTru4 GCA_011762595.1_mTurTru1.mat.Y 9739
176 Indo-pacific bottlenose dolphin Cetartiodactyla Tursiops aduncus HLturAdu1 GCA_003227395.1 79784
177 Indo-pacific bottlenose dolphin Cetartiodactyla Tursiops aduncus DNA zoo Tursiops aduncus 79784
178 common bottlenose dolphin Cetartiodactyla Tursiops truncatus Oct. 2011 (Baylor Ttru_1.4/turTru2) 9739
179 common bottlenose dolphin Cetartiodactyla Tursiops truncatus HLturTru3 GCA_001922835.1_NIST_Tur_tru_v1 9739
180 pig Cetartiodactyla Sus scrofa Feb. 2017 (Sscrofa11.1/susScr11) 9823
181 okapi Cetartiodactyla Okapia johnstoni DNA zoo Okapia johnstoni 86973
182 Masai giraffe Cetartiodactyla Giraffa tippelskirchi HLgirTip1 GCA_001651235.1_ASM165123v1 439328
183 water buffalo Cetartiodactyla Bubalus bubalis HLbubBub2 GCA_003121395.1 89462
184 zebu cattle Cetartiodactyla Bos indicus HLbosInd2 GCA_002933975.1 9915
185 cow Cetartiodactyla Bos taurus Apr. 2018 (ARS-UCD1.2/bosTau9) 9913
186 wild yak Cetartiodactyla Bos mutus HLbosMut2 GCA_007646595.3 72004
187 greater kudu Cetartiodactyla Tragelaphus strepsiceros HLtraStr1 GCA_006410795.1 9946
188 aoudad Cetartiodactyla Ammotragus lervia HLammLer1 GCA_002201775.1_ALER1.0 9899
189 goat Cetartiodactyla Capra hircus HLcapHir2 GCA_001704415.1_ARS1 9925
190 wild goat Cetartiodactyla Capra aegagrus HLcapAeg1 GCA_000765075.1 9923
191 chiru Cetartiodactyla Pantholops hodgsonii May 2013 (PHO1.0/panHod1) 59538
192 white-tailed deer Cetartiodactyla Odocoileus virginianus HLodoVir3 GCA_014726795.1 9874
193 bighorn sheep Cetartiodactyla Ovis canadensis HLoviCan2 GCA_004026945.1_OviCan_v1_BIUU 37174
194 white-tailed deer Cetartiodactyla Odocoileus virginianus DNA zoo Odocoileus virginianus 9874
195 sheep Cetartiodactyla Ovis aries HLoviAri5 GCA_011170295.1 9940
196 Pere David's deer Cetartiodactyla Elaphurus davidianus HLelaDav1 GCA_002443075.1_Milu1.0 43332
197 argali Cetartiodactyla Ovis ammon HLoviAmm1 GCA_003121645.1 30527
198 North Atlantic right whale Artiodactyla Eubalaena glacialis DNA zoo Eubalaena glacialis 27606
199 North Pacific right whale Artiodactyla Eubalaena japonica HLeubJap1 GCA_004363455.1_EubJap_v1_BIUU 302098
200 minke whale Artiodactyla Balaenoptera acutorostrata scammoni Oct. 2013 (BalAcu1.0/balAcu1) 310752
201 humpback whale Artiodactyla Megaptera novaeangliae HLmegNov1 GCA_004329385.1 9773
202 Fin whale Artiodactyla Balaenoptera physalus HLbalPhy1 GCA_008795845.1 9770
203 bowhead whale Artiodactyla Balaena mysticetus HLbalMys1 27602
204 Blue whale Artiodactyla Balaenoptera musculus HLbalMus1 GCA_009873245.1 9771
205 pygmy Bryde's whale Artiodactyla Balaenoptera edeni DNA zoo Balaenoptera edeni 9769
206 Sowerby's beaked whale Artiodactyla Mesoplodon bidens HLmesBid1 GCA_004027085.1_MesBid_v1_BIUU 48745
207 Indus River dolphin Artiodactyla Platanista minor HLplaMin1 GCA_004363435.1_PlaMin_v1_BIUU 48752
208 Cuvier's beaked whale Artiodactyla Ziphius cavirostris HLzipCav1 GCA_004364475.1_ZipCav_v1_BIUU 9760
209 boutu Artiodactyla Inia geoffrensis HLlniGeo1 GCA_004363515.1_IniGeo_v1_BIUU 9725
210 narwhal Artiodactyla Monodon monoceros HLmonMon1 GCA_005190385.2 40151
211 Yangtze finless porpoise Artiodactyla Neophocaena asiaeorientalis asiaeorientalis HLneoAsi1 GCA_003031525.1_Neophocaena_asiaeorientalis_V1 1706337
212 pygmy sperm whale Artiodactyla Kogia breviceps HLkogBre1 GCA_004363705.1_KogBre_v1_BIUU 27615
213 vaquita Artiodactyla Phocoena sinus HLphoSin1 GCA_008692025.1 42100
214 franciscana Artiodactyla Pontoporia blainvillei HLponBla1 GCA_011754075.1 48723
215 Lama pacos huacaya Artiodactyla Vicugna pacos huacaya HLvicPacHua3 GCA_000767525.1_Vi_pacos_V1.0 273913
216 llama Artiodactyla Lama glama DNA zoo Lama glama 9844
217 melon-headed whale Artiodactyla Peponocephala electra DNA zoo Peponocephala electra 103596
218 long-finned pilot whale Artiodactyla Globicephala melas HLgloMel1 GCA_006547405.1 9731
219 Pacific white-sided dolphin Artiodactyla Lagenorhynchus obliquidens HLlagObl1 GCA_003676395.1 90247
220 Vicugna mensalis Artiodactyla Vicugna vicugna mensalis HLvicVicMen1 GCA_013265495.1 273917
221 guanaco Artiodactyla Lama guanicoe cacsilensis HLlamGuaCac1 GCA_013239625.1 273908
222 llama Artiodactyla Lama glama chaku HLlamGlaCha1 GCA_013239585.1 273914
223 Chacoan peccary Artiodactyla Catagonus wagneri HLcatWag1 GCA_004024745.2_CatWag_v2_BIUU_UCD 51154
224 giraffe Artiodactyla Giraffa camelopardalis HLgirCam1 GCA_006408565.1 9894
225 giraffe Artiodactyla Giraffa camelopardalis DNA zoo Giraffa camelopardalis 9894
226 African buffalo Artiodactyla Syncerus caffer HLsynCaf1 GCA_902500845.1 9970
227 Bos bison bison Artiodactyla Bison bison bison Oct. 2014 (Bison_UMD1.0/bisBis1) 43346
228 Chinese forest musk deer Artiodactyla Moschus berezovskii HLmosBer1 GCA_006459085.1 68408
229 Siberian musk deer Artiodactyla Moschus moschiferus HLmosMos1 GCA_004024705.2 68415
230 alpine musk deer Artiodactyla Moschus chrysogaster HLmosChr1 GCA_006461725.1 68412
231 Yarkand deer Artiodactyla Cervus hanglu yarkandensis HLcerHanYar1 GCA_010411085.1 84702
232 gaur Artiodactyla Bos gaurus HLbosGau1 GCA_014182915.1 9904
233 gayal Artiodactyla Bos frontalis HLbosFro1 GCA_007844835.1_NRC_Mithun_1 30520
234 white-lipped deer Artiodactyla Przewalskium albirostris HLprzAlb1 GCA_006408465.1 1088058
235 roan antelope Artiodactyla Hippotragus equinus HLhipEqu1 GCA_016433095.1 37186
236 Harvey's duiker Artiodactyla Cephalophus harveyi HLcepHar1 GCA_006410635.1 129224
237 sable antelope Artiodactyla Hippotragus niger niger HLhipNig1 GCA_006942125.1 82127
238 domestic yak Artiodactyla Bos grunniens HLbosGru1 GCA_005887515.2 30521
239 scimitar-horned oryx Artiodactyla Oryx dammah DNA zoo Oryx dammah 59534
240 bush duiker Artiodactyla Sylvicapra grimmia HLsylGri1 GCA_006408735.1 119562
241 Maxwell's duiker Artiodactyla Philantomba maxwellii HLphiMax1 GCA_006410695.1 907741
242 gemsbok Artiodactyla Oryx gazella HLoryGaz1 GCA_003945745.1 9958
243 pronghorn Artiodactyla Antilocapra americana HLantAme1 GCA_007570785.1 9891
244 Reeves' muntjac Artiodactyla Muntiacus reevesi HLmunRee1 GCA_008787405.1 9886
245 black muntjac Artiodactyla Muntiacus crinifrons HLmunCri1 GCA_006408485.1 71854
246 Central European red deer Artiodactyla Cervus elaphus hippelaphus HLcerEla1 GCA_002197005.1 46360
247 lesser kudu Artiodactyla Tragelaphus imberbis HLtraImb1 GCA_006410775.1 9947
248 brindled gnu Artiodactyla Connochaetes taurinus DNA zoo Connochaetes taurinus 9927
249 bushbuck Artiodactyla Tragelaphus scriptus HLtraScr1 GCA_006410495.1 66440
250 waterbuck Artiodactyla Kobus ellipsiprymnus HLkobEll1 GCA_006410655.1 9962
251 muntjak Artiodactyla Muntiacus muntjak HLmunMun1 GCA_008782695.1 9888
252 topi Artiodactyla Damaliscus lunatus HLdamLun1 GCA_006408505.1 9929
253 bighorn sheep Artiodactyla Ovis canadensis canadensis HLoviCan1 GCA_001039535.1 112262
254 lechwe Artiodactyla Kobus leche leche HLkobLecLec1 GCA_014926565.1 91880
255 Eastern roe deer Artiodactyla Capreolus pygargus HLcapPyg1 GCA_012922965.1 48560
256 Eurasian elk Artiodactyla Alces alces HLalcAlc1 GCA_007570765.1 9852
257 Cobus hunteri Artiodactyla Beatragus hunteri HLbeaHun1 GCA_004027495.1_BeaHun_v1_BIUU 59527
258 impala Artiodactyla Aepyceros melampus HLaepMel1 GCA_006408695.1 9897
259 mule deer Artiodactyla Odocoileus hemionus hemionus HLodoHem1 GCA_004115125.1 9877
260 Bohar reedbuck Artiodactyla Redunca redunca HLredRed1 GCA_006410935.1 59556
261 Siberian ibex Artiodactyla Capra sibirica HLcapSib1 GCA_003182615.2 72544
262 porcupine caribou Artiodactyla Rangifer tarandus granti HLranTarGra2 GCA_014898785.1 191431
263 reindeer Artiodactyla Rangifer tarandus HLranTar1 GCA_004026565.1_RanTarSib_v1_BIUU 9870
264 klipspringer Artiodactyla Oreotragus oreotragus HLoreOre1 GCA_006410675.1 66444
265 Chinese water deer Artiodactyla Hydropotes inermis HLhydIne1 GCA_006459105.1 9883
266 snow sheep Artiodactyla Ovis nivicola lydekkeri HLoviNivLyd1 GCA_903231385.1 1867112
267 suni Artiodactyla Neotragus moschatus HLneoMos1 GCA_006410615.1 66442
268 white-tailed deer Artiodactyla Odocoileus virginianus texanus HLodoVir1 GCA_002102435.1_Ovir.te_1.0 9880
269 Nilgiri tahr Artiodactyla Hemitragus hylocrius HLhemHyl1 GCA_004026825.1_HemHyl_v1_BIUU 330464
270 Asiatic mouflon Artiodactyla Ovis orientalis HLoviOri1 GCA_014523465.1 469796
271 royal antelope Artiodactyla Neotragus pygmaeus HLneoPyg1 GCA_006410875.1 1027985
272 Grant's gazelle Artiodactyla Nanger granti HLnanGra1 GCA_006408635.1 27591
273 Przewalski's gazelle Artiodactyla Procapra przewalskii HLproPrz1 GCA_006410515.1 157668
274 steenbok Artiodactyla Raphicerus campestris HLrapCam1 GCA_006410735.1 59544
275 Thomson's gazelle Artiodactyla Eudorcas thomsonii HLeudTho1 GCA_006408755.1 69308
276 springbok Artiodactyla Antidorcas marsupialis HLantMar1 GCA_006408585.1 59523
277 gerenuk Artiodactyla Litocranius walleri HLlitWal1 GCA_006410535.1 69311
278 Kirk's dik-dik Artiodactyla Madoqua kirkii HLmadKir1 GCA_006408675.1 66434
279 Hog deer Artiodactyla Axis porcinus HLaxiPor1 GCA_003798545.1 57737
280 Java mouse-deer Artiodactyla Tragulus javanicus HLtraJav1 GCA_004024965.2 9849
281 lesser mouse-deer Artiodactyla Tragulus kanchil HLtraKan1 GCA_006408655.1 1088131
282 mountain goat Artiodactyla Oreamnos americanus HLoreAme1 GCA_009758055.1 34873
283 saiga antelope Artiodactyla Saiga tatarica HLsaiTat1 GCA_004024985.1_SaiTat_v1_BIUU 34875
284 Alpine ibex Artiodactyla Capra ibex HLcapIbe1 GCA_006410555.1 72542
285 Hoffmann's two-fingered sloth Xenarthra Choloepus hoffmanni DNA zoo Choloepus hoffmanni 9358
286 southern two-toed sloth Xenarthra Choloepus didactylus HLchoDid2 GCF_015220235.1_mChoDid1.pri 27675
287 southern two-toed sloth Xenarthra Choloepus didactylus HLchoDid1 GCA_004027855.1_ChoDid_v1_BIUU 27675
288 nine-banded armadillo Xenarthra Dasypus novemcinctus Dec. 2011 (Baylor/dasNov3) 9361
289 giant anteater Xenarthra Myrmecophaga tridactyla HLmyrTri1 GCA_004026745.1_MyrTri_v1_BIUU 71006
290 southern tamandua Xenarthra Tamandua tetradactyla HLtamTet1 GCA_004025105.1_TamTet_v1_BIUU 48850
291 Southern three-banded armadillo Xenarthra Tolypeutes matacus HLtolMat1 GCA_004025125.1_TolMat_v1_BIUU 183749
292 Chinese rufous horseshoe bat Chiroptera Rhinolophus sinicus HLrhiSin1 GCA_001888835.1_ASM188883v1 89399
293 great roundleaf bat Chiroptera Hipposideros armiger HLhipArm1 GCA_001890085.1_ASM189008v1 186990
294 black flying fox Chiroptera Pteropus alecto Aug 2012 (ASM32557v1/pteAle1) 9402
295 greater horseshoe bat Chiroptera Rhinolophus ferrumequinum HLrhiFer5/Bat1K 59479
296 Bonin flying fox Chiroptera Pteropus pselaphon HLptePse1 GCA_014363405.1 1496133
297 Brazilian free-tailed bat Chiroptera Tadarida brasiliensis HLtadBra1 GCA_004025005.1_TadBra_v1_BIUU 9438
298 large flying fox Chiroptera Pteropus vampyrus HLpteVam2 GCA_000151845.2 132908
299 Malagasy flying fox Chiroptera Pteropus rufus DNA zoo Pteropus rufus 196297
300 Indian flying fox Chiroptera Pteropus giganteus HLpteGig1 GCA_902729225.1 143291
301 Malagasy straw-colored fruit bat Chiroptera Eidolon dupreanum DNA zoo Eidolon dupreanum 58063
302 straw-colored fruit bat Chiroptera Eidolon helvum DNA zoo Eidolon helvum 77214
303 Cantor's roundleaf bat Chiroptera Hipposideros galeritus HLhipGal1 GCA_004027415.1_HipGal_v1_BIUU 58069
304 lesser short-nosed fruit bat Chiroptera Cynopterus brachyotis HLcynBra1 GCA_009793145.1 58060
305 lesser dawn bat Chiroptera Eonycteris spelaea HLeonSpe1 GCA_003508835.1 58065
306 Leschenault's rousette Chiroptera Rousettus leschenaultii HLrouLes1 GCA_015472975.1 9408
307 Egyptian rousette Chiroptera Rousettus aegyptiacus HLrouAeg4/Bat1K 9407
308 Madagascan rousette Chiroptera Rousettus madagascariensis DNA zoo Rousettus madagascariensis 77223
309 Indian false vampire Chiroptera Megaderma lyra HLmegLyr2 GCA_004026885.1_MegLyr_v1_BIUU 9413
310 Pallas's mastiff bat Chiroptera Molossus molossus HLmolMol2/Bat1K 27622
311 long-tongued fruit bat Chiroptera Macroglossus sobrinus HLmacSob1 GCA_004027375.1_MacSob_v1_BIUU 326083
312 Schreibers' long-fingered bat Chiroptera Miniopterus schreibersii HLminSch1 GCA_004026525.1_MinSch_v1_BIUU 9433
313 Miniopterus schreibersii natalensis Chiroptera Miniopterus natalensis HLminNat1 GCA_001595765.1 291302
314 hog-nosed bat Chiroptera Craseonycteris thonglongyai HLcraTho1 GCA_004027555.1_CraTho_v1_BIUU 208972
315 Antillean ghost-faced bat Chiroptera Mormoops blainvillei HLmorBla1 GCA_004026545.1_MorMeg_v1_BIUU 118852
316 Parnell's mustached bat Chiroptera Pteronotus parnellii Sep. 2013 (ASM46540v1/ptePar1) 59476
317 big brown bat Chiroptera Eptesicus fuscus Jul 2012 (EptFus1.0/eptFus1) 29078
318 greater mouse-eared bat Chiroptera Myotis myotis HLmyoMyo6/Bat1K 51298
319 Brandt's bat Chiroptera Myotis brandtii 28 Jun 2013 (ASM41265v1/myoBra1) 109478
320 common vampire bat Chiroptera Desmodus rotundus HLdesRot2/Bat1K 9430
321 California big-eared bat Chiroptera Macrotus californicus HLmacCal1 GCA_007922815.1 9419
322 Northern long-eared myotis Chiroptera Myotis septentrionalis DNA zoo Myotis septentrionalis 258941
323 little brown bat Chiroptera Myotis lucifugus DNA zoo Myotis lucifugus 59463
324 little brown bat Chiroptera Myotis lucifugus Jul. 2010 (Broad Institute Myoluc2.0/myoLuc2) 59463
325 Lesser long-nosed bat Chiroptera Leptonycteris yerbabuenae HLlepYer1/GIGADB 700936
326 Vespertilio Davidii Chiroptera Myotis davidii Aug 2012 (ASM32734v1/myoDav1) 225400
327 Schizostoma hirsutum Chiroptera Micronycteris hirsuta HLmicHir1 GCA_004026765.1_MicHir_v1_BIUU 148065
328 tailed tailless bat Chiroptera Anoura caudifer HLanoCau1 GCA_004027475.1_AnoCau_v1_BIUU 27642
329 Murina feae Chiroptera Murina aurata feae HLmurAurFea1 GCA_004026665.1_MurFea_v1_BIUU 1453894
330 greater bulldog bat Chiroptera Noctilio leporinus HLnocLep1 GCA_004026585.1_NocLep_v1_BIUU 94963
331 Seba's short-tailed bat Chiroptera Carollia perspicillata HLcarPer3 GCA_004027735.1_CarPer_v1_BIUU 40233
332 pale spear-nosed bat Chiroptera Phyllostomus discolor HLphyDis3/Bat1K 89673
333 stripe-headed round-eared bat Chiroptera Tonatia saurophila HLtonSau1 GCA_004024845.1_TonSau_v1_BIUU 171122
334 Jamaican fruit-eating bat Chiroptera Artibeus jamaicensis HLartJam1 GCA_004027435.1_ArtJam_v1_BIUU 9417
335 Jamaican fruit-eating bat Chiroptera Artibeus jamaicensis HLartJam2 GCA_014825515.1 9417
336 Honduran yellow-shouldered bat Chiroptera Sturnira hondurensis HLstuHon1 GCA_014824575.1 192404
337 hoary bat Chiroptera Aeorestes cinereus HLaeoCin1 GCA_011751065.1 257879
338 pallid bat Chiroptera Antrozous pallidus HLantPal1 GCA_007922775.1 9440
339 evening bat Chiroptera Nycticeius humeralis HLnycHum2 GCA_007922795.1 27670
340 red bat Chiroptera Lasiurus borealis HLlasBor1 GCA_004026805.1_LasBor_v1_BIUU 258930
341 Kuhl's pipistrelle Chiroptera Pipistrellus kuhlii HLpipKuh2/Bat1K 59472
342 common pipistrelle Chiroptera Pipistrellus pipistrellus HLpipPip1 GCA_004026625.1_PipPip_v1_BIUU 59474
343 common pipistrelle Chiroptera Pipistrellus pipistrellus HLpipPip2 GCA_903992545.1 59474
344 gray squirrel Glires Sciurus carolinensis HLsciCar1 GCA_902686445.1 30640
345 Eurasian red squirrel Glires Sciurus vulgaris HLsciVul1 GCA_902686455.1_mSciVul1.1 55149
346 South African ground squirrel Glires Xerus inauris HLxerIna1 GCA_004024805.1_XerIna_v1_BIUU 234690
347 mountain beaver Glires Aplodontia rufa HLaplRuf1 GCA_004027875.1_AplRuf_v1_BIUU 51342
348 yellow-bellied marmot Glires Marmota flaviventris HLmarFla1 GCA_003676075.2 93162
349 Alpine marmot Glires Marmota marmota marmota HLmarMar1 GCF_001458135.1_marMar2.1 9994
350 Vancouver Island marmot Glires Marmota vancouverensis HLmarVan1 GCA_005458795.1 93167
351 Himalayan marmot Glires Marmota himalayana HLmarHim1 GCA_005280165.1 93163
352 Daurian ground squirrel Glires Spermophilus dauricus HLspeDau1 GCA_002406435.1_ASM240643v1 99837
353 woodchuck Glires Marmota monax HLmarMon1 GCA_901343595.1_MONAX5 9995
354 woodchuck Glires Marmota monax HLmarMon2 GCA_014533835.1 9995
355 Arctic ground squirrel Glires Urocitellus parryii HLuroPar1 GCA_003426925.1 9999
356 Gunnison's prairie dog Glires Cynomys gunnisoni HLcynGun1 GCA_011316645.1 45479
357 thirteen-lined ground squirrel Glires Ictidomys tridecemlineatus Nov. 2011 (Broad/speTri2) 43179
358 Fat dormouse Glires Glis glis HLgliGli1 GCA_004027185.1_GliGli_v1_BIUU 41261
359 springhare Glires Pedetes capensis HLpedCap1 GCA_007922755.1 10023
360 American beaver Glires Castor canadensis DNA zoo Castor canadensis 51338
361 woodland dormouse Glires Graphiurus murinus HLgraMur1 GCA_004027655.1_GraMur_v1_BIUU 51346
362 Mountain hare Glires Lepus timidus HLlepTim1 GCA_009760805.1 62621
363 snowshoe hare Glires Lepus americanus HLlepAme1 GCA_004026855.1_LepAme_v1_BIUU 48086
364 European rabbit Glires Oryctolagus cuniculus cuniculus HLoryCunCun4 GCA_013371645.1 568996
365 rabbit Glires Oryctolagus cuniculus Apr. 2009 (Broad/oryCun2) 9986
366 rabbit Glires Oryctolagus cuniculus HLoryCun3 GCA_009806435.1 9986
367 brush rabbit Glires Sylvilagus bachmani DNA zoo Sylvilagus bachmani 365149
368 crested porcupine Glires Hystrix cristata HLhysCri1 GCA_004026905.1_HysCri_v1_BIUU 10137
369 North American porcupine Glires Erethizon dorsatum HLereDor1 GCA_006547115.1 34844
370 Brazilian porcupine Glires Coendou prehensilis DNA zoo Coendou prehensilis 187985
371 hazel dormouse Glires Muscardinus avellanarius HLmusAve1 GCA_004027005.1_MusAve_v1_BIUU 39082
372 naked mole-rat Glires Heterocephalus glaber Jan. 2012 (Broad HetGla_female_1.0/hetGla2) 10181
373 Damara mole-rat Glires Fukomys damarensis HLfukDam2 GCA_012274545.1 885580
374 Upper Galilee mountains blind mole rat Glires Nannospalax galili Jun 2014 (S.galili_v1.0/nanGal1) 1026970
375 long-tailed chinchilla Glires Chinchilla lanigera May 2012 (ChiLan1.0/chiLan1) 34839
376 punctate agouti Glires Dasyprocta punctata HLdasPun1 GCA_004363535.1_DasPun_v1_BIUU 34846
377 northern gundi Glires Ctenodactylus gundi HLcteGun1 GCA_004027205.1_CteGun_v1_BIUU 10166
378 Gobi jerboa Glires Allactaga bullata HLallBul1 GCA_004027895.1_AllBul_v1_BIUU 1041416
379 Stephens's kangaroo rat Glires Dipodomys stephensi HLdipSte1 GCA_004024685.1_DipSte_v1_BIUU 323379
380 Ord's kangaroo rat Glires Dipodomys ordii Dec. 2014 (Dord_2.0/dipOrd2) 10020
381 hoary bamboo rat Glires Rhizomys pruinosus HLrhiPru1 GCA_009823505.1 53275
382 pacarana Glires Dinomys branickii HLdinBra1 GCA_004027595.1_DinBra_v1_BIUU 108858
383 lesser Egyptian jerboa Glires Jaculus jaculus May 2012 (JacJac1.0/jacJac1) 51337
384 meadow jumping mouse Glires Zapus hudsonius HLzapHud1 GCA_004024765.1_ZapHud_v1_BIUU 160400
385 Patagonian cavy Glires Dolichotis patagonum HLdolPat1 GCA_004027295.1_DolPat_v1_BIUU 29091
386 Pacific pocket mouse Glires Perognathus longimembris pacificus HLperLonPac1 GCA_004363475.1_PerLonPac_v1_BIUU 214514
387 capybara Glires Hydrochoerus hydrochaeris HLhydHyd1 GCA_004027455.1_HydHyd_v1_BIUU 10149
388 American pika Glires Ochotona princeps May 2012 (OchPri3.0/ochPri3) 9978
389 Brazilian guinea pig Glires Cavia aperea Jan. 2014 (CavAp1.0/cavApe1) 37548
390 dassie-rat Glires Petromus typicus HLpetTyp1 GCA_004026965.1_PetTyp_v1_BIUU 10183
391 Montane guinea pig Glires Cavia tschudii HLcavTsc1 GCA_004027695.1_CavTsc_v1_BIUU 143287
392 domestic guinea pig Glires Cavia porcellus Feb. 2008 (Broad/cavPor3) 10141
393 Greater cane rat Glires Thryonomys swinderianus HLthrSwi1 GCA_004025085.1_ThrSwi_v1_BIUU 10169
394 degu Glires Octodon degus Apr 2012 (OctDeg1.0/octDeg1) 10160
395 Gambian giant pouched rat Glires Cricetomys gambianus HLcriGam1 GCA_004027575.1_CriGam_v1_BIUU 10085
396 desert woodrat Glires Neotoma lepida HLneoLep1 GCA_001675575.1 56216
397 social tuco-tuco Glires Ctenomys sociabilis HLcteSoc1 GCA_004027165.1_CteSoc_v1_BIUU 43321
398 nutria Glires Myocastor coypus HLmyoCoy1 GCA_004027025.1_MyoCoy_v1_BIUU 10157
399 northern rock mouse Glires Peromyscus nasutus DNA zoo Peromyscus nasutus 97212
400 Chinese hamster Glires Cricetulus griseus HLcriGri3 GCA_003668045.1 10029
401 Hesperomys crinitus Glires Peromyscus crinitus DNA zoo Peromyscus crinitus 144753
402 muskrat Glires Ondatra zibethicus HLondZib1 GCA_004026605.1_OndZib_v1_BIUU 10060
403 Peromyscus californicus subsp. insignis Glires Peromyscus californicus insignis HLperCal2 GCA_007827085.2 564181
404 cactus mouse Glires Peromyscus eremicus HLperEre1 GCA_902702925.1 42410
405 southern grasshopper mouse Glires Onychomys torridus HLonyTor1 GCA_903995425.1 38674
406 golden hamster Glires Mesocricetus auratus Mar 2013 (MesAur1.0/mesAur1) 10036
407 white-footed mouse Glires Peromyscus leucopus HLperLeu1 GCA_004664715.1 10041
408 Northern mole vole Glires Ellobius talpinus HLellTal1 GCA_001685095.1_ETalpinus_0.1 329620
409 oldfield mouse Glires Peromyscus polionotus subgriseus HLperPol1 GCA_003704135.2 369710
410 prairie deer mouse Glires Peromyscus maniculatus bairdii HLperManBai2 GCA_003704035.1 230844
411 hispid cotton rat Glires Sigmodon hispidus HLsigHis1 GCA_004025045.1_SigHis_v1_BIUU 42415
412 Transcaucasian mole vole Glires Ellobius lutescens HLellLut1 GCA_001685075.1_ASM168507v1 39086
413 Bank vole Glires Myodes glareolus HLmyoGla2 GCA_902806735.1 447135
414 Eurasian water vole Glires Arvicola amphibius HLarvAmp1 GCA_903992535.1 1047088
415 fat sand rat Glires Psammomys obesus HLpsaObe1 GCA_002215935.2 48139
416 golden spiny mouse Glires Acomys russatus HLacoRus1 GCA_903995435.1 60746
417 African woodland thicket rat Glires Grammomys surdaster HLgraSur1 GCA_004785775.1 491861
418 African grass rat Glires Arvicanthis niloticus HLarvNil1 GCA_011762505.1_mArvNil1.pat.X 61156
419 root vole Glires Microtus oeconomus HLmicOec1 GCA_007455595.1 64717
420 short-tailed field vole Glires Microtus agrestis HLmicAgr2 GCA_902806775.1 29092
421 reed vole Glires Microtus fortis HLmicFor1 GCA_014885135.1 100897
422 Egyptian spiny mouse Glires Acomys cahirinus HLacoCah1 GCA_004027535.1_AcoCah_v1_BIUU 10068
423 Common vole Glires Microtus arvalis HLmicArv1 GCA_007455615.1 47230
424 prairie vole Glires Microtus ochrogaster Oct. 2012 (MicOch1.0/micOch1) 79684
425 great gerbil Glires Rhombomys opimus HLrhoOpi1 GCA_010120015.1 186474
426 southern multimammate mouse Glires Mastomys coucha HLmasCou1 GCA_008632895.1 35658
427 Mongolian gerbil Glires Meriones unguiculatus HLmerUng1 GCA_002204375.1 10047
428 black rat Glires Rattus rattus HLratRat7 GCA_011064425.1 10117
429 Norway rat Glires Rattus norvegicus HLratNor7 GCA_015227675.1 10116
430 Norway rat Glires Rattus norvegicus Jul. 2014 (RGSC 6.0/rn6) 10116
431 shrew mouse Glires Mus pahari HLmusPah1 GCA_900095145.2 10093
432 Ryukyu mouse Glires Mus caroli HLmusCar1 GCA_900094665.2_CAROLI_EIJ_v1.1 10089
433 steppe mouse Glires Mus spicilegus HLmusSpi1 GCA_003336285.1 10103
434 house mouse Glires Mus musculus Jun. 2020 (GRCm39/mm39) 10090
435 house mouse Glires Mus musculus Dec. 2011 (GRCm38/mm10) 10090
436 western wild mouse Glires Mus spretus HLmusSpr1 GCA_001624865.1_SPRET_EiJ_v1 10096
437 European woodmouse Glires Apodemus sylvaticus HLapoSyl1 GCA_001305905.1 10129
438 dugong Afrotheria Dugong dugon HLdugDug1 GCA_015147995.1 29137
439 Florida manatee Afrotheria Trichechus manatus latirostris Oct. 2011 (Broad v1.0/triMan1) 127582
440 Asiatic elephant Afrotheria Elephas maximus DNA zoo Elephas maximus 9783
441 African savanna elephant Afrotheria Loxodonta africana HLloxAfr4/Broad Institute/loxAfr4 9785
442 aardvark Afrotheria Orycteropus afer afer May 2012 (OryAfe1.0/oryAfe1) 1230840
443 Steller's sea cow Afrotheria Hydrodamalis gigas HLhydGig1 GCA_013391785.1 63631
444 Cape golden mole Afrotheria Chrysochloris asiatica Aug 2012 (ChrAsi1.0/chrAsi1) 185453
445 yellow-spotted hyrax Afrotheria Heterohyrax brucei HLhetBru1 GCA_004026845.1_HetBruBak_v1_BIUU 77598
446 Cape rock hyrax Afrotheria Procavia capensis HLproCap3 GCA_004026925.2 9813
447 Cape elephant shrew Afrotheria Elephantulus edwardii Aug 2012 (EleEdw1.0/eleEdw1) 28737
448 small Madagascar hedgehog Afrotheria Echinops telfairi Nov. 2012 (Broad/echTel2) 9371
449 Talazac's shrew tenrec Afrotheria Microgale talazaci HLmicTal1 GCA_004026705.1_MicTal_v1_BIUU 176115
450 common wombat Metatheria Vombatus ursinus HLvomUrs1 GCA_900497805.2 29139
451 koala Metatheria Phascolarctos cinereus HLphaCin1 GCA_002099425.1 38626
452 Agile Gracile Mouse Opossum Metatheria Gracilinanus agilis HLgraAgi1 GCA_016433145.1 191870
453 common brushtail Metatheria Trichosurus vulpecula HLtriVul1 GCA_011100635.1_mTriVul1.pri 9337
454 North American opossum Metatheria Didelphis virginiana DNA zoo Didelphis virginiana 9267
455 ground cuscus Metatheria Phalanger gymnotis DNA zoo Phalanger gymnotis 65615
456 gray short-tailed opossum Metatheria Monodelphis domestica Oct. 2006 (Broad/monDom5) 13616
457 Leadbeater's possum Metatheria Gymnobelideus leadbeateri HLgymLea1 GCA_011680675.1 38618
458 Tasmanian wolf Metatheria Thylacinus cynocephalus HLthyCyn1 GCA_007646695.1 9275
459 coppery ringtail possum Metatheria Pseudochirops cupreus DNA zoo Pseudochirops cupreus 37702
460 eastern gray kangaroo Metatheria Macropus giganteus DNA zoo Macropus giganteus 9317
461 golden ringtail possum Metatheria Pseudochirops corinnae DNA zoo Pseudochirops corinnae 65629
462 western gray kangaroo Metatheria Macropus fuliginosus DNA zoo Macropus fuliginosus 9316
463 tammar wallaby Metatheria Macropus eugenii DNA zoo Macropus eugenii 9315
464 red kangaroo Metatheria Osphranter rufus DNA zoo Osphranter rufus 9321
465 Western ringtail oppossum Metatheria Pseudocheirus occidentalis DNA zoo Pseudocheirus occidentalis 656515
466 tammar wallaby Metatheria Macropus eugenii Sep. 2009 (TWGS Meug_1.1/macEug2) 9315
467 yellow-footed antechinus Metatheria Antechinus flavipes HLantFla1 GCA_016432865.1_AdamAnt 38775
468 Tasmanian devil Metatheria Sarcophilus harrisii HLsarHar2 GCA_902635505.1 9305
469 platypus Monotremata Ornithorhynchus anatinus HLornAna3 GCA_004115215.1 9258
470 Australian echidna Monotremata Tachyglossus aculeatus HLtacAcu1 GCA_015852505.1 9261

Table 1. Genome assemblies included in the 470-way Conservation track.

Display Conventions and Configuration

In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the size 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 human 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. 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. Missing sequence in any assembly is highlighted in the track display by regions of yellow when zoomed out and by Ns when displayed at base level. The following conventions are used:

  • Single line: No bases in the aligned species. Possibly due to a lineage-specific insertion between the aligned blocks in the human genome or a lineage-specific deletion between the aligned blocks in the aligning species.
  • Double line: Aligning species has one or more unalignable bases in the gap region. Possibly due to excessive evolutionary distance between species or independent indels in the region between the aligned blocks in both species.
  • Pale yellow coloring: Aligning species has Ns in the gap region. Reflects uncertainty in the relationship between the DNA of both species, due to lack of sequence in relevant portions of the aligning species.

Genomic Breaks

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

  • Vertical blue bar: Represents a discontinuity that persists indefinitely on either side, e.g. a large region of DNA on either side of the bar comes from a different chromosome in the aligned species due to a large scale rearrangement.
  • Green square brackets: Enclose shorter alignments consisting of DNA from one genomic context in the aligned species nested inside a larger chain of alignments from a different genomic context. The alignment within the brackets may represent a short misalignment, a lineage-specific insertion of a transposon in the human genome that aligns to a paralogous copy somewhere else in the aligned species, or other similar occurrence.

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 human sequence at those alignment positions relative to the longest non-human 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:

  • No codon translation: The gene annotation is not used; the bases are displayed without translation.
  • Use default species reading frames for translation: The annotations from the genome displayed in the Default species to establish reading frame pull-down menu are used to translate all the aligned species present in the alignment.
  • Use reading frames for species if available, otherwise no translation: Codon translation is performed only for those species where the region is annotated as protein coding.
  • Use reading frames for species if available, otherwise use default species: Codon translation is done on those species that are annotated as being protein coding over the aligned region using species-specific annotation; the remaining species are translated using the default species annotation.

Codon translation uses the following gene tracks as the basis for translation:

Gene TrackSpecies
RefSeq Genesaardvark, American pika, Amur tiger, Angolan colobus, big brown bat, black flying fox, black snub-nosed monkey, Bolivian squirrel monkey, Brandt's bat, Cape elephant shrew, Cape golden mole, cattle, chimpanzee, Chinese tree shrew, Coquerel's sifaka, degu, dog, domestic cat, domestic guinea pig, drill, European shrew, Florida manatee, golden hamster, gray mouse lemur, green monkey, Hawaiian monk seal, horse, house mouse, house mouse, human, killer whale, lesser Egyptian jerboa, little brown bat, long-tailed chinchilla, Ma's night monkey, minke whale, naked mole-rat, nine-banded armadillo, Northern sea otter, Norway rat, Ord's kangaroo rat, Pacific walrus, Panamanian white-faced capuchin, Philippine tarsier, pig, pig-tailed macaque, polar bear, prairie vole, Przewalski's horse, pygmy chimpanzee, rabbit, Rhesus monkey, small Madagascar hedgehog, small-eared galago, sooty mangabey, southern white rhinoceros, star-nosed mole, Sumatran orangutan, thirteen-lined ground squirrel, Upper Galilee mountains blind mole rat, Vespertilio Davidii, Weddell seal, western European hedgehog, western lowland gorilla, Yangtze River dolphin
Ensembl GenesBos bison bison, Brazilian guinea pig, dog, gray short-tailed opossum, northern tree shrew
Xeno RefGenealpaca, black lemur, Chinese pangolin, common bottlenose dolphin, proboscis monkey, Sclater's lemur, Southern sea otter, tammar wallaby
no annotationAfrican buffalo, African grass rat, African hunting dog, African hunting dog, African savanna elephant, African woodland thicket rat, Agile Gracile Mouse Opossum, Allen's swamp monkey, Alpine ibex, Alpine marmot, alpine musk deer, American beaver, American black bear, American black bear, American mink, Amur leopard cat, antarctic fur seal, Antarctic minke whale, Antillean ghost-faced bat, aoudad, Arabian camel, Arctic fox, Arctic ground squirrel, argali, Asian black bear, Asian palm civet, Asiatic elephant, Asiatic mouflon, Asiatic tapir, Asiatic tapir, ass, Australian echidna, aye-aye, babakoto, Bactrian camel, banded mongoose, Bank vole, bearded seal, beluga whale, bighorn sheep, bighorn sheep, black muntjac, black rat, black rhinoceros, black-footed cat, black-handed spider monkey, Blue whale, Bohar reedbuck, Bolivian squirrel monkey, Bolivian titi, Bonin flying fox, boutu, bowhead whale, Brazilian free-tailed bat, Brazilian porcupine, Brazilian tapir, brindled gnu, brown lemur, brush rabbit, bush duiker, bushbuck, Cacomistle, cactus mouse, California big-eared bat, California sea lion, Canada lynx, Cantor's roundleaf bat, Cape rock hyrax, capybara, Central European red deer, Chacoan peccary, cheetah, Chinese forest musk deer, Chinese hamster, Chinese pangolin, Chinese rufous horseshoe bat, Chinese water deer, chiru, Clouded leopard, Cobus hunteri, common bottlenose dolphin, common bottlenose dolphin, common brushtail, common pipistrelle, common pipistrelle, common vampire bat, Common vole, common wombat, coppery ringtail possum, Coquerel's mouse lemur, crab-eating macaque, crested porcupine, Cuvier's beaked whale, Damara mole-rat, dassie-rat, Daurian ground squirrel, De Brazza's monkey, desert woodrat, dingo, domestic ferret, domestic yak, donkey, dugong, dwarf mongoose, eastern gray kangaroo, eastern mole, Eastern roe deer, Egyptian rousette, Egyptian spiny mouse, Equus burchelli boehmi, ermine, Eurasian elk, Eurasian red squirrel, Eurasian river otter, Eurasian water vole, European polecat, European rabbit, European woodmouse, evening bat, Fat dormouse, fat sand rat, Fin whale, fossa, franciscana, Francois's langur, Gambian giant pouched rat, gaur, gayal, gelada, gemsbok, gerenuk, giant anteater, giant otter, giant otter, giant panda, giraffe, giraffe, goat, Gobi jerboa, golden ringtail possum, golden snub-nosed monkey, golden spiny mouse, gracile shrew mole, Grant's gazelle, gray seal, gray squirrel, great gerbil, great roundleaf bat, greater bamboo lemur, greater bulldog bat, Greater cane rat, greater horseshoe bat, greater Indian rhinoceros, greater kudu, greater mouse-eared bat, grey whale, grizzly bear, ground cuscus, guanaco, Gunnison's prairie dog, Hanuman langur, harbor porpoise, harbor porpoise, harbor seal, Harvey's duiker, hazel dormouse, Hesperomys crinitus, Himalayan marmot, hippopotamus, hippopotamus, Hispaniolan solenodon, hispid cotton rat, hoary bamboo rat, hoary bat, Hoffmann's two-fingered sloth, Hog deer, hog-nosed bat, Honduran yellow-shouldered bat, humpback whale, Iberian mole, impala, Indian false vampire, Indian flying fox, Indo-pacific bottlenose dolphin, Indo-pacific bottlenose dolphin, Indo-pacific humpbacked dolphin, Indus River dolphin, jaguar, jaguar, jaguarundi, Jamaican fruit-eating bat, Jamaican fruit-eating bat, Japanese macaque, Java mouse-deer, kinkajou, Kirk's dik-dik, klipspringer, koala, Kuhl's pipistrelle, Lama pacos huacaya, large flying fox, Leadbeater's possum, lechwe, leopard, Leschenault's rousette, lesser dawn bat, Lesser dwarf lemur, lesser kudu, Lesser long-nosed bat, lesser mouse-deer, lesser panda, lesser short-nosed fruit bat, lion, little brown bat, llama, llama, long-finned pilot whale, long-tongued fruit bat, Madagascan rousette, Malagasy flying fox, Malagasy straw-colored fruit bat, Malayan pangolin, Malayan pangolin, mandrill, mantled howler monkey, Masai giraffe, Maxwell's duiker, meadow jumping mouse, meerkat, meerkat, melon-headed whale, Miniopterus schreibersii natalensis, Mona monkey, Mongolian gerbil, mongoose lemur, Montane guinea pig, mountain beaver, mountain goat, Mountain hare, mouse lemur, mule deer, muntjak, Murina feae, muskrat, narwhal, Nilgiri tahr, North American badger, North American opossum, North American porcupine, North Atlantic right whale, North Pacific right whale, Northern American river otter, Northern elephant seal, northern fur seal, Northern giant mouse lemur, northern gundi, Northern long-eared myotis, Northern mole vole, northern rock mouse, Northern rufous mouse lemur, northern white rhinoceros, northern white-cheeked gibbon, Norway rat, nutria, okapi, oldfield mouse, olive baboon, pacarana, Pacific pocket mouse, Pacific white-sided dolphin, pale spear-nosed bat, Pallas's mastiff bat, pallid bat, Parnell's mustached bat, Patagonian cavy, Pere David's deer, Peromyscus californicus subsp. insignis, platypus, porcupine caribou, prairie deer mouse, pronghorn, Przewalski's gazelle, puma, punctate agouti, pygmy Bryde's whale, pygmy marmoset, pygmy sperm whale, rabbit, raccoon, ratel, red bat, red fox, red guenon, red kangaroo, Red shanked douc langur, reed vole, Reeves' muntjac, reindeer, Ring-tailed lemur, roan antelope, root vole, royal antelope, Ryukyu mouse, sable, sable antelope, saiga antelope, Schizostoma hirsutum, Schreibers' long-fingered bat, scimitar-horned oryx, Sclater's lemur, Seba's short-tailed bat, sheep, short-tailed field vole, shrew mouse, Siberian ibex, Siberian musk deer, silvery gibbon, slow loris, snow sheep, snowshoe hare, social tuco-tuco, South African ground squirrel, Southern elephant seal, southern grasshopper mouse, southern multimammate mouse, southern tamandua, Southern three-banded armadillo, southern two-toed sloth, southern two-toed sloth, Sowerby's beaked whale, Spanish lynx, sperm whale, sperm whale, spotted hyena, springbok, springhare, steenbok, Steller sea lion, Steller's sea cow, Stephens's kangaroo rat, steppe mouse, straw-colored fruit bat, stripe-headed round-eared bat, striped hyena, Sumatran rhinoceros, Sunda flying lemur, suni, tailed tailless bat, Talazac's shrew tenrec, tamarin, tammar wallaby, Tasmanian devil, Tasmanian wolf, Thomson's gazelle, topi, Transcaucasian mole vole, Tree pangolin, Tree pangolin, tufted capuchin, Ugandan red Colobus, Vancouver Island marmot, vaquita, Vicugna mensalis, walrus, water buffalo, waterbuck, western gray kangaroo, Western ringtail oppossum, western spotted skunk, western wild mouse, white-faced saki, white-footed mouse, white-fronted capuchin, white-lipped deer, White-nosed coati, white-tailed deer, white-tailed deer, white-tailed deer, white-tufted-ear marmoset, Wild Bactrian camel, wild goat, wild yak, wolverine, woodchuck, woodchuck, woodland dormouse, Yangtze finless porpoise, Yarkand deer, yellow-bellied marmot, yellow-footed antechinus, yellow-spotted hyrax, zebu cattle,
Table 2. Gene tracks used for codon translation.


Pairwise alignments with the human 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. The scoring matrix and parameters for pairwise alignment and chaining were tuned for each species based on phylogenetic distance from the reference. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net.

Phylogenetic Tree Model

The 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 470-way alignment (msa_view). The 4d sites were derived from the RefSeq (Reviewed+Coding) gene set, filtered to select single-coverage long transcripts.

This same tree model was used in the phyloP calculations; however, the background frequencies were modified to maintain reversibility. The resulting tree model: all species.

PhyloP Conservation

The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements ( 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).


This track was created using the following programs:

  • Alignment tools: lastz (formerly blastz) and multiz by Minmei Hou, Scott Schwartz and Webb Miller of the Penn State Bioinformatics Group
  • Chaining and Netting: axtChain, chainNet by Jim Kent at UCSC
  • Conservation scoring: phastCons, phyloP, phyloFit, tree_doctor, msa_view and other programs in PHAST by Adam Siepel at Cold Spring Harbor Laboratory (original development done at the Haussler lab at UCSC).
  • MAF Annotation tools: mafAddIRows by Brian Raney, UCSC; mafAddQRows by Richard Burhans, Penn State; genePredToMafFrames by Mark Diekhans, UCSC
  • Tree image generator: phyloPng by Galt Barber, UCSC
  • Conservation track display: Kate Rosenbloom, Hiram Clawson (wiggle display), and Brian Raney (gap annotation and codon framing) at UCSC


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


Cooper GM, Stone EA, Asimenos G, NISC Comparative Sequencing Program., Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005 Jul;15(7):901-13. PMID: 15965027; PMC: PMC1172034; DOI: 10.1101/gr.3577405

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, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351. DOI: 10.1007/0-387-27733-1_12

Siepel A, Pollard KS, and Haussler D. New methods for detecting lineage-specific selection. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006), pp. 190-205. DOI: 10.1007/11732990_17