Cactus 241-way Track Settings
 
Cactus Alignment & Conservation of Zoonomia Placental Mammals (241 Species)   (All Comparative Genomics tracks)

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Species selection:  + - default

  Primate  + -

pan_troglodytes
pan_paniscus
gorilla_gorilla
pongo_abelii
gibbon
macaca_fascicularis
macaca_mulatta
papio_anubis
macaca_nemestrina
mandrillus_leucophaeus
nasalis_larvatus
erythrocebus_patas
cercopithecus_neglectus
chlorocebus_sabaeus
semnopithecus_entellus
rhinopithecus_roxellana
rhinopithecus_bieti
pygathrix_nemaeus
angolan colobus
piliocolobus_tephrosceles
cercocebus_atys
pithecia_pithecia
ateles_geoffroyi
aotus_nancymaae
callicebus_donacophilus
alouatta_palliata
cebus_albifrons
white-faced sapajou
saguinus_imperator
squirrel monkey
callithrix_jacchus
daubentonia_madagascariensis
lemur_catta
eulemur_fulvus
eulemur_flavifrons
propithecus_coquereli
indri_indri
cheirogaleus_medius
mirza_coquereli
microcebus_murinus
nycticebus_coucang
bushbaby

  Carnivore  + -

neomonachus_schauinslandi
leptonychotes_weddellii
mirounga_angustirostris
pacific walrus
zalophus_californianus
ursus_maritimus
ailuropoda_melanoleuca
panthera_tigris
panthera_onca
panthera_pardus
acinonyx_jubatus
puma_concolor
felis_nigripes
cryptoprocta_ferox
felis_catus
ailurus_fulgens
lycaon_pictus
canis_lupus_familiaris
canis_lupus
vulpes_lagopus
hyaena_hyaena
paradoxurus_hermaphroditus
mellivora_capensis
enhydra_lutris
pteronura_brasiliensis
helogale_parvula
mungos_mungo
spilogale_gracilis
suricata_suricatta
mustela_putorius

  Cetartiodactyla  + -

eubalaena_japonica
eschrichtius_robustus
balaenoptera_bonaerensis
balaenoptera_acutorostrata
ziphius_cavirostris
monodon_monoceros
delphinapterus_leucas
mesoplodon_bidens
killer whale
lipotes_vexillifer
tursiops_truncatus
neophocaena_asiaeorientalis
phocoena_phocoena
platanista_gangetica
inia_geoffrensis
kogia_breviceps
hippopotamus_amphibius
camelus_dromedarius
camelus_ferus
camelus_bactrianus
vicugna_pacos
sus_scrofa
giraffa_tippelskirchi
okapia_johnstoni
elaphurus_davidianus
catagonus_wagneri
bubalus_bubalis
rangifer_tarandus
odocoileus_virginianus
bison_bison
bosMut1
bos_indicus
bos_taurus
moschus_moschiferus
pantholops_hodgsonii
beatragus_hunteri
ovis_canadensis
ovis_aries
antilocapra_americana
hemitragus_hylocrius
ammotragus_lervia
capra_hircus
capra_aegagrus
saiga_tatarica
tragulus_javanicus

  Chiroptera  + -

hipposideros_armiger
rhinolophus_sinicus
black flying-fox
pteropus_vampyrus
tadarida_brasiliensis
hipposideros_galeritus
eidHel1
miniopterus_schreibersii
miniopterus_natalensis
macroglossus_sobrinus
rousettus_aegyptiacus
eptesicus_fuscus
myoBra1
microbat
myotis_myotis
david's myotis (bat)
mormoops_blainvillei
megaderma_lyra
ptePar1
desmodus_rotundus
craseonycteris_thonglongyai
anoura_caudifer
murina_feae
tonatia_saurophila
carollia_perspicillata
pipistrellus_pipistrellus
micronycteris_hirsuta
noctilio_leporinus
lasiurus_borealis
artibeus_jamaicensis

  Rodents  + -

glis_glis
graphiurus_murinus
xerus_inauris
spermophilus_dauricus
castor_canadensis
squirrel
aplodontia_rufa
marmota_marmota
hystrix_cristata
heterocephalus_glaber
muscardinus_avellanarius
cuniculus_paca
chinchilla
dasyprocta_punctata
fukDam1
ctenodactylus_gundi
dinomys_branickii
dolichotis_patagonum
hydrochoerus_hydrochaeris
cavia_tschudii
cavia_porcellus
cavApe1
dipOrd2
dipodomys_stephensi
nannospalax_galili
thryonomys_swinderianus
octodon_degus
allactaga_bullata
petromus_typicus
perognathus_longimembris
zapus_hudsonius
jaculus_jaculus
ctenomys_sociabilis
capromys_pilorides
myocastor_coypus
cricetomys_gambianus
peromyscus_maniculatus
onychomys_torridus
cricetulus_griseus
ellobius_talpinus
mesocricetus_auratus
ellobius_lutescens
psammomys_obesus
meriones_unguiculatus
prairie vole
ondatra_zibethicus
acomys_cahirinus
sigmodon_hispidus
mus_musculus
mus_caroli
mus_spretus
mus_pahari
rattus_norvegicus

  Mammals  + -

galeopterus_variegatus
ceratotherium_simum_cottoni
ceratotherium_simum
diceros_bicornis
dicerorhinus_sumatrensis
tapirus_indicus
tapirus_terrestris
equus_asinus
equus_przewalskii
equus_caballus
tupaia_tana
chinese tree shrew
trichechus_manatus
loxodonta_africana
manis_pentadactyla
manis_javanica
choloepus_didactylus
choloepus_hoffmanni
tolypeutes_matacus
chaetophractus_vellerosus
oryctolagus_cuniculus
lepus_americanus
orycteropus_afer
dasypus_novemcinctus
myrmecophaga_tridactyla
tamandua_tetradactyla
solenodon_paradoxus
scalopus_aquaticus
procavia_capensis
heterohyrax_brucei
chrysochloris_asiatica
uropsilus_gracilis
condylura_cristata
ochotona_princeps
echinops_telfairi
cape elephant shrew
erinaceus_europaeus
shrew
microgale_talazaci
crocidura_indochinensis

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 Basewise Cons  PhyloP Basewise Conservation of Zoonomia 241 Placental Mammals   Schema 
 
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 Cactus Align  Cactus Alignments of Zoonomia 241 Placental Mammals   Schema 


new Note: Released Sep. 13, 2021

Downloads for data in this track are available:

  • Cactus alignments (MAF format), and phylogenetic trees, and PhyloP conservation (WIG and bigWig format)

Description

This track shows multiple alignments of 241 vertebrate species and measurements of evolutionary conservation from the Zoonomia Project.

The multiple alignments were generated using the Cactus comparative genomics alignment system. Cactus produces reference-free, whole-genome multiple alignments.

The base-wise conservation scores are computed using phyloP from the PHAST package, for all species. This version was prepared by Michael Dong (Uppsala U) with an improved neutral model incorporating better versions of ancestral repeats.

For genome assemblies not available in the genome browser, there are alternative assembly hub genome browsers. 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 (see Gap Annotation, below).

count common
name
CLADE group scientific
name
sequencing
source
NCBI
assembly
species
status
1 Cape golden mole AFROSORICIDA Chrysochloridae Chrysochloris asiatica 1. Zoonomia GCA_004027935.1 LC
2 Small madagascar hedgehog AFROSORICIDA Tenrecidae Echinops telfairi 2. Existing assembly GCF_000313985.1 LC
3 Talazac's shrew tenrec AFROSORICIDA Tenrecidae Microgale talazaci 1. Zoonomia GCA_004026705.1 LC
4 Cheetah CARNIVORA Felidae Acinonyx jubatus 2. Existing assembly GCF_001443585.1 CR
5 Giant panda CARNIVORA Ursidae Ailuropoda melanoleuca 2. Existing assembly GCA_002007445.1 VU
6 Lesser panda CARNIVORA Ailuridae Ailurus fulgens 2. Existing assembly GCA_002007465.1 EN
7 Domestic dog CARNIVORA Canidae Canis lupus familiaris 2. Existing assembly GCF_000002285.3 LC
8 Domestic dog (village dog) CARNIVORA Canidae Canis lupus familiaris 1. Zoonomia GCA_004027395.1 LC
9 Fossa CARNIVORA Eupleridae Cryptoprocta ferox 1. Zoonomia GCA_004023885.1 VU
10 Sea otter CARNIVORA Mustelidae Enhydra lutris 2. Existing assembly GCF_002288905.1 EN
11 Domestic cat CARNIVORA Felidae Felis catus 2. Existing assembly GCF_000181335.2 LC
12 Black-footed cat CARNIVORA Felidae Felis nigripes 1. Zoonomia GCA_004023925.1 VU
13 Dwarf mongoose CARNIVORA Herpestidae Helogale parvula 1. Zoonomia GCA_004023845.1 LC
14 Striped hyena CARNIVORA Hyaenidae Hyaena hyaena 1. Zoonomia GCA_004023945.1 NT
15 Weddell seal CARNIVORA Phocidae Leptonychotes weddellii 2. Existing assembly GCF_000349705.1 LC
16 African hunting dog CARNIVORA Canidae Lycaon pictus 2. Existing assembly GCA_001887905.1 EN
17 Honey badger CARNIVORA Mustelidae Mellivora capensis 1. Zoonomia GCA_004024625.1 LC
18 Northern elephant seal CARNIVORA Phocidae Mirounga angustirostris 1. Zoonomia GCA_004023865.1 LC
19 South African banded mongoose CARNIVORA Herpestidae Mungos mungo 1. Zoonomia GCA_004023785.1 LC
20 Domestic ferret CARNIVORA Mustelidae Mustela putorius 2. Existing assembly GCF_000239315.1 LC
21 Hawaiian monk seal CARNIVORA Phocidae Neomonachus schauinslandi 2. Existing assembly GCA_002201575.1 EN
22 Pacific walrus CARNIVORA Odobenidae Odobenus rosmarus 2. Existing assembly GCF_000321225.1 DD
23 Jaguar CARNIVORA Felidae Panthera onca 1. Zoonomia GCA_004023805.1 NT
24 Leopard CARNIVORA Felidae Panthera pardus 2. Existing assembly GCA_001857705.1 VU
25 Amur tiger CARNIVORA Felidae Panthera tigris 2. Existing assembly GCF_000464555.1 EN
26 Asian palm civet CARNIVORA Viverridae Paradoxurus hermaphroditus 1. Zoonomia GCA_004024585.1 LC
27 Giant otter CARNIVORA Mustelidae Pteronura brasiliensis 1. Zoonomia GCA_004024605.1 EN
28 Puma CARNIVORA Felidae Puma concolor 2. Existing assembly GCF_003327715.1 LC
29 Western spotted skunk CARNIVORA Mephitidae Spilogale gracilis 1. Zoonomia GCA_004023965.1 LC
30 Meerkat CARNIVORA Herpestidae Suricata suricatta 1. Zoonomia GCA_004023905.1 LC
31 Polar bear CARNIVORA Ursidae Ursus maritimus 2. Existing assembly GCF_000687225.1 VU
32 Arctic fox CARNIVORA Canidae Vulpes lagopus 1. Zoonomia GCA_004023825.1 LC
33 California sea lion CARNIVORA Otariidae Zalophus californianus 1. Zoonomia GCA_004024565.1 LC
34 Aoudad CETARTIODACTYLA Bovidae Ammotragus lervia 2. Existing assembly GCA_002201775.1 VU
35 Pronghorn CETARTIODACTYLA Antilocapridae Antilocapra americana 1. Zoonomia GCA_004027515.1 LC
36 Minke whale CETARTIODACTYLA Balaenopteridae Balaenoptera acutorostrata 2. Existing assembly GCF_000493695.1 LC
37 Antarctic minke whale CETARTIODACTYLA Balaenopteridae Balaenoptera bonaerensis 2. Existing assembly GCA_000978805.1 DD
38 Hirola CETARTIODACTYLA Bovidae Beatragus hunteri 1. Zoonomia GCA_004027495.1 CR
39 American bison CETARTIODACTYLA Bovidae Bison bison 2. Existing assembly GCF_000754665.1 NT
40 Zebu cattle CETARTIODACTYLA Bovidae Bos indicus 2. Existing assembly GCA_000247795.2 LC
41 Wild yak CETARTIODACTYLA Bovidae Bos mutus 2. Existing assembly GCF_000298355.1 VU
42 Cattle CETARTIODACTYLA Bovidae Bos taurus 2. Existing assembly GCF_000003205.7 LC
43 Water buffalo CETARTIODACTYLA Bovidae Bubalus bubalis 2. Existing assembly GCF_000471725.1 LC
44 Bactrian camel CETARTIODACTYLA Camelidae Camelus bactrianus 2. Existing assembly GCF_000767855.1 LC
45 Arabian camel CETARTIODACTYLA Camelidae Camelus dromedarius 2. Existing assembly GCF_000767585.1 LC
46 Wild bactrian camel CETARTIODACTYLA Camelidae Camelus ferus 2. Existing assembly GCF_000311805.1 CR
47 Wild goat CETARTIODACTYLA Bovidae Capra aegagrus 2. Existing assembly GCA_000978405.1 VU
48 Goat CETARTIODACTYLA Bovidae Capra hircus 2. Existing assembly GCF_001704415.1 LC
49 Chacoan peccary CETARTIODACTYLA Tayassuidae Catagonus wagneri 1. Zoonomia GCA_004024745.1 EN
50 Beluga whale CETARTIODACTYLA Monodontidae Delphinapterus leucas 2. Existing assembly GCF_002288925.1 LC
51 Pere david's deer CETARTIODACTYLA Cervidae Elaphurus davidianus 2. Existing assembly GCA_002443075.1 CR
52 Grey whale CETARTIODACTYLA Eschrichtiidae Eschrichtius robustus 1. Zoonomia GCA_004363415.1 LC
53 North Pacific right whale CETARTIODACTYLA Balaenidae Eubalaena japonica 1. Zoonomia GCA_004363455.1 EN
54 Giraffe CETARTIODACTYLA Giraffidae Giraffa tippelskirchi 2. Existing assembly GCA_001651235.1 VU
55 Nilgiri tahr CETARTIODACTYLA Bovidae Hemitragus hylocrius 1. Zoonomia GCA_004026825.1 EN
56 Hippopotamus CETARTIODACTYLA Hippopotamidae Hippopotamus amphibius 1. Zoonomia GCA_004027065.1 VU
57 Amazon river dolphin CETARTIODACTYLA Iniidae Inia geoffrensis 1. Zoonomia GCA_004363515.1 DD
58 Pygmy sperm whale CETARTIODACTYLA Physeteridae Kogia breviceps 1. Zoonomia GCA_004363705.1 DD
59 Yangtze river dolphin CETARTIODACTYLA Iniidae Lipotes vexillifer 2. Existing assembly GCF_000442215.1 CR
60 Sowerby's beaked whale CETARTIODACTYLA Ziphiidae Mesoplodon bidens 1. Zoonomia GCA_004027085.1 DD
61 Narwhal CETARTIODACTYLA Monodontidae Monodon monoceros 1. Zoonomia GCA_004026685.1 LC
62 Siberian musk deer CETARTIODACTYLA Moschidae Moschus moschiferus 1. Zoonomia GCA_004024705.1 VU
63 Yangtze finless porpoise CETARTIODACTYLA Phocoenidae Neophocaena asiaeorientalis 2. Existing assembly GCA_003031525.1 EN
64 White-tailed deer CETARTIODACTYLA Cervidae Odocoileus virginianus 2. Existing assembly GCA_002102435.1 LC
65 Okapi CETARTIODACTYLA Giraffidae Okapia johnstoni 2. Existing assembly GCA_001660835.1 EN
66 Killer whale CETARTIODACTYLA Delphinidae Orcinus orca 2. Existing assembly GCF_000331955.2 DD
67 Sheep CETARTIODACTYLA Bovidae Ovis aries 2. Existing assembly GCF_000298735.2 LC
68 Peninsular bighorn sheep CETARTIODACTYLA Bovidae Ovis canadensis cremnobates 1. Zoonomia GCA_004026945.1 EN
69 Chiru CETARTIODACTYLA Bovidae Pantholops hodgsonii 2. Existing assembly GCF_000400835.1 NT
70 Harbor porpoise CETARTIODACTYLA Phocoenidae Phocoena phocoena 1. Zoonomia GCA_004363495.1 LC
71 Indus river dolphin CETARTIODACTYLA Platanistidae Platanista gangetica minor 1. Zoonomia GCA_004363435.1 EN
72 Siberian reindeer CETARTIODACTYLA Cervidae Rangifer tarandus 1. Zoonomia GCA_004026565.1 VU
73 Russian saiga CETARTIODACTYLA Bovidae Saiga tatarica tatarica 1. Zoonomia GCA_004024985.1 CR
74 Pig CETARTIODACTYLA Suidae Sus scrofa 2. Existing assembly GCF_000003025.5 LC
75 Java lesser chevrotain CETARTIODACTYLA Tragulidae Tragulus javanicus 1. Zoonomia GCA_004024965.1 DD
76 Bottlenose dolphin CETARTIODACTYLA Delphinidae Tursiops truncatus 2. Existing assembly GCA_001922835.1 LC
77 Alpaca CETARTIODACTYLA Camelidae Vicugna pacos 2. Existing assembly GCA_000767525.1 LC
78 Cuvier's beaked whale CETARTIODACTYLA Ziphiidae Ziphius cavirostris 1. Zoonomia GCA_004364475.1 LC
79 Tailed tailless bat CHIROPTERA Phyllostomidae Anoura caudifer 1. Zoonomia GCA_004027475.1 LC
80 Jamacian fruit-eating bat CHIROPTERA Phyllostomidae Artibeus jamaicensis 1. Zoonomia GCA_004027435.1 LC
81 Seba's short-tailed bat CHIROPTERA Phyllostomidae Carollia perspicillata 1. Zoonomia GCA_004027735.1 LC
82 Bumblebee bat CHIROPTERA Craseonycteridae Craseonycteris thonglongyai 1. Zoonomia GCA_004027555.1 VU
83 Common vampire bat CHIROPTERA Phyllostomidae Desmodus rotundus 2. Existing assembly GCA_002940915.2 LC
84 Straw-colored fruit bat CHIROPTERA Pteropodidae Eidolon helvum 2. Existing assembly GCA_000465285.1 NT
85 Big brown bat CHIROPTERA Vespertilionidae Eptesicus fuscus 2. Existing assembly GCF_000308155.1 LC
86 Great roundleaf bat CHIROPTERA Hipposideridae Hipposideros armiger 2. Existing assembly GCA_001890085.1 LC
87 Cantor's leaf-nosed bat CHIROPTERA Hipposideridae Hipposideros galeritus 1. Zoonomia GCA_004027415.1 LC
88 Eastern red bat CHIROPTERA Vespertilionidae Lasiurus borealis 1. Zoonomia GCA_004026805.1 LC
89 Long-tongued fruit bat CHIROPTERA Pteropodidae Macroglossus sobrinus 1. Zoonomia GCA_004027375.1 LC
90 Greater false vampire bat CHIROPTERA Megadermatidae Megaderma lyra 1. Zoonomia GCA_004026885.1 LC
91 Hairy big-eared bat CHIROPTERA Phyllostomidae Micronycteris hirsuta 1. Zoonomia GCA_004026765.1 LC
92 Bats CHIROPTERA Vespertilionidae Miniopterus natalensis 2. Existing assembly GCF_001595765.1 LC
93 Common bent-wing bat CHIROPTERA Vespertilionidae Miniopterus schreibersii 1. Zoonomia GCA_004026525.1 NT
94 Ghost-faced bat CHIROPTERA Mormoopidae Mormoops blainvillei 1. Zoonomia GCA_004026545.1 LC
95 Ashy-gray tube-nosed bat CHIROPTERA Vespertilionidae Murina feae 1. Zoonomia GCA_004026665.1 LC
96 Brandt's bat CHIROPTERA Vespertilionidae Myotis brandtii 2. Existing assembly GCF_000412655.1 LC
97 Bats CHIROPTERA Vespertilionidae Myotis davidii 2. Existing assembly GCF_000327345.1 LC
98 Little brown bat CHIROPTERA Vespertilionidae Myotis lucifugus 2. Existing assembly GCF_000147115.1 LC
99 Greater mouse-eared bat CHIROPTERA Vespertilionidae Myotis myotis 1. Zoonomia GCA_004026985.1 LC
100 Greater bulldog bat CHIROPTERA Noctilionidae Noctilio leporinus 1. Zoonomia GCA_004026585.1 LC
101 Common pipistrelle CHIROPTERA Vespertilionidae Pipistrellus pipistrellus 1. Zoonomia GCA_004026625.1 LC
102 Parnell's mustached bat CHIROPTERA Mormoopidae Pteronotus parnellii 2. Existing assembly GCA_000465405.1 LC
103 Black flying fox CHIROPTERA Pteropodidae Pteropus alecto 2. Existing assembly GCF_000325575.1 LC
104 Large flying fox CHIROPTERA Pteropodidae Pteropus vampyrus 2. Existing assembly GCF_000151845.1 NT
105 Chinese rufous horseshoe bat CHIROPTERA Rhinolophidae Rhinolophus sinicus 2. Existing assembly GCA_001888835.1 LC
106 Egyptian fruit bat CHIROPTERA Pteropodidae Rousettus aegyptiacus 1. Zoonomia GCA_004024865.1 LC
107 Mexican free-tailed bat CHIROPTERA Molossidae Tadarida brasiliensis 1. Zoonomia GCA_004025005.1 LC
108 Stripe-headed round-eared bat CHIROPTERA Phyllostomidae Tonatia saurophila 1. Zoonomia GCA_004024845.1 LC
109 Screaming hairy armadillo CINGULATA Dasypodidae Chaetophractus vellerosus 1. Zoonomia GCA_004027955.1 LC
110 Nine-banded armadillo CINGULATA Dasypodidae Dasypus novemcinctus 2. Existing assembly GCF_000208655.1 LC
111 Southern three-banded armadillo CINGULATA Dasypodidae Tolypeutes matacus 1. Zoonomia GCA_004025125.1 NT
112 Sunda flying lemur DERMOPTERA Cynocephalidae Galeopterus variegatus 1. Zoonomia GCA_004027255.1 LC
113 Star-nosed mole EULIPOTYPHLA Talpidae Condylura cristata 2. Existing assembly GCF_000260355.1 LC
114 Indochinese shrew EULIPOTYPHLA Soricidae Crocidura indochinensis 1. Zoonomia GCA_004027635.1 LC
115 Western european hedgehog EULIPOTYPHLA Erinaceidae Erinaceus europaeus 2. Existing assembly GCF_000296755.1 LC
116 Eastern mole EULIPOTYPHLA Talpidae Scalopus aquaticus 1. Zoonomia GCA_004024925.1 LC
117 Hispaniolan solenodon EULIPOTYPHLA Solenodontidae Solenodon paradoxus 1. Zoonomia GCA_004363575.1 EN
118 European shrew EULIPOTYPHLA Soricidae Sorex araneus 2. Existing assembly GCF_000181275.1 LC
119 Gracile shrew-like mole EULIPOTYPHLA Talpidae Uropsilus gracilis 1. Zoonomia GCA_004024945.1 LC
120 African yellow-spotted rock hyrax HYRACOIDEA Procaviidae Heterohyrax brucei 1. Zoonomia GCA_004026845.1 LC
121 South African rock hyrax HYRACOIDEA Procaviidae Procavia capensis 1. Zoonomia GCA_004026925.1 LC
122 Snowshoe hare LAGOMORPHA Leporidae Lepus americanus 1. Zoonomia GCA_004026855.1 LC
123 American pika LAGOMORPHA Ochotonidae Ochotona princeps 2. Existing assembly GCF_000292845.1 LC
124 Rabbit LAGOMORPHA Leporidae Oryctolagus cuniculus 2. Existing assembly GCF_000003625.3 NT
125 Cape elephant shrew MACROSCELIDEA Macroscelididae Elephantulus edwardii 1. Zoonomia GCA_004027355.1 LC
126 Southern white rhinoceros PERISSODACTYLA Rhinocerotidae Ceratotherium simum 2. Existing assembly GCF_000283155.1 NT
127 Northern white rhino PERISSODACTYLA Rhinocerotidae Ceratotherium simum cottoni 1. Zoonomia GCA_004027795.1 CR
128 Sumatran rhinoceros PERISSODACTYLA Rhinocerotidae Dicerorhinus sumatrensis 2. Existing assembly GCA_002844835.1 CR
129 Black rhinocerous PERISSODACTYLA Rhinocerotidae Diceros bicornis 1. Zoonomia GCA_004027315.1 CR
130 Ass PERISSODACTYLA Equidae Equus asinus 2. Existing assembly GCF_001305755.1 LC
131 Horse PERISSODACTYLA Equidae Equus caballus 2. Existing assembly GCF_000002305.2 LC
132 Przewalski's horse PERISSODACTYLA Equidae Equus przewalskii 2. Existing assembly GCF_000696695.1 EN
133 Malayan tapir PERISSODACTYLA Tapiridae Tapirus indicus 1. Zoonomia GCA_004024905.1 EN
134 South American tapir PERISSODACTYLA Tapiridae Tapirus terrestris 1. Zoonomia GCA_004025025.1 VU
135 Malayan pangolin PHOLIDOTA Manidae Manis javanica 2. Existing assembly GCF_001685135.1 CR
136 Chinese pangolin PHOLIDOTA Manidae Manis pentadactyla 2. Existing assembly GCA_000738955.1 CR
137 Linnaeus's two toed sloth PILOSA Megalonychidae Choloepus didactylus 1. Zoonomia GCA_004027855.1 LC
138 Hoffmann's two-fingered sloth PILOSA Megalonychidae Choloepus hoffmanni 2. Existing assembly GCA_000164785.2 LC
139 Giant anteater PILOSA Myrmecophagidae Myrmecophaga tridactyla 1. Zoonomia GCA_004026745.1 VU
140 Southern tamandua PILOSA Myrmecophagidae Tamandua tetradactyla 1. Zoonomia GCA_004025105.1 LC
141 Mexican howler monkey PRIMATES Atelidae Alouatta palliata mexicana 1. Zoonomia GCA_004027835.1 CR
142 Ma's night monkey PRIMATES Aotidae Aotus nancymaae 2. Existing assembly GCA_000952055.2 VU
143 Geoffroy's spider monkey PRIMATES Atelidae Ateles geoffroyi 1. Zoonomia GCA_004024785.1 EN
144 White-eared titi PRIMATES Pitheciidae Callicebus donacophilus 1. Zoonomia GCA_004027715.1 LC
145 White-tufted-ear marmoset PRIMATES Cebidae Callithrix jacchus 2. Existing assembly GCA_002754865.1 LC
146 White-fronted capuchin PRIMATES Cebidae Cebus albifrons 1. Zoonomia GCA_004027755.1 LC
147 White-faced sapajou PRIMATES Cebidae Cebus capucinus 2. Existing assembly GCF_001604975.1 LC
148 Sooty mangabey PRIMATES Cercopithecidae Cercocebus atys 2. Existing assembly GCF_000955945.1 NT
149 De brazza's monkey PRIMATES Cercopithecidae Cercopithecus neglectus 1. Zoonomia GCA_004027615.1 LC
150 Fat-tailed dwarf lemur PRIMATES Cheirogaleidae Cheirogaleus medius 1. Zoonomia GCA_004024725.1 LC
151 Green monkey PRIMATES Cercopithecidae Chlorocebus sabaeus 2. Existing assembly GCF_000409795.2 LC
152 Angolan colobus PRIMATES Cercopithecidae Colobus angolensis 2. Existing assembly GCF_000951035.1 VU
153 Aye-aye PRIMATES Daubentoniidae Daubentonia madagascariensis 1. Zoonomia GCA_004027145.1 EN
154 Patas monkey PRIMATES Cercopithecidae Erythrocebus patas 1. Zoonomia GCA_004027335.1 LC
155 Sclater's lemur PRIMATES Lemuridae Eulemur flavifrons 2. Existing assembly GCA_001262665.1 CR
156 Common brown lemur PRIMATES Lemuridae Eulemur fulvus 1. Zoonomia GCA_004027275.1 NT
157 Western lowland gorilla PRIMATES Hominidae Gorilla gorilla 2. Existing assembly GCA_900006655.3 CR
158 Human PRIMATES Hominidae Homo sapiens 2. Existing assembly GCA_000001405.27 LC
159 Indri PRIMATES Indridae Indri indri 1. Zoonomia GCA_004363605.1 CR
160 Ring tailed lemur PRIMATES Lemuridae Lemur catta 1. Zoonomia GCA_004024665.1 EN
161 Crab-eating macaque PRIMATES Cercopithecidae Macaca fascicularis 2. Existing assembly GCF_000364345.1 DD
162 Rhesus monkey PRIMATES Cercopithecidae Macaca mulatta 2. Existing assembly GCF_000772875.2 LC
163 Pig-tailed macaque PRIMATES Cercopithecidae Macaca nemestrina 2. Existing assembly GCF_000956065.1 VU
164 Drill PRIMATES Cercopithecidae Mandrillus leucophaeus 2. Existing assembly GCF_000951045.1 EN
165 Gray mouse lemur PRIMATES Cheirogaleidae Microcebus murinus 2. Existing assembly GCA_000165445.3 LC
166 Coquerel's giant mouse lemur PRIMATES Cheirogaleidae Mirza coquereli 1. Zoonomia GCA_004024645.1 EN
167 Proboscis monkey PRIMATES Cercopithecidae Nasalis larvatus 1. Zoonomia GCA_004027105.1 EN
168 Northern white-cheeked gibbon PRIMATES Hylobatidae Nomascus leucogenys 2. Existing assembly GCF_000146795.2 CR
169 Sunda slow loris PRIMATES Lorisidae Nycticebus coucang 1. Zoonomia GCA_004027815.1 VU
170 Small-eared galago PRIMATES Galagidae Otolemur garnettii 2. Existing assembly GCF_000181295.1 LC
171 Pygmy chimpanzee PRIMATES Hominidae Pan paniscus 2. Existing assembly GCF_000258655.2 EN
172 Chimpanzee PRIMATES Hominidae Pan troglodytes 2. Existing assembly GCA_002880755.3 EN
173 Olive baboon PRIMATES Cercopithecidae Papio anubis 2. Existing assembly GCA_000264685.2 LC
174 Ugandan red colobus PRIMATES Cercopithecidae Piliocolobus tephrosceles 2. Existing assembly GCA_002776525.1 EN
175 White-faced saki PRIMATES Pitheciidae Pithecia pithecia 1. Zoonomia GCA_004026645.1 LC
176 Sumatran orangutan PRIMATES Hominidae Pongo abelii 2. Existing assembly GCA_002880775.3 CR
177 Coquerel's sifaka PRIMATES Indridae Propithecus coquereli 2. Existing assembly GCF_000956105.1 EN
178 Red-shanked douc PRIMATES Cercopithecidae Pygathrix nemaeus 1. Zoonomia GCA_004024825.1 EN
179 Black snub-nosed monkey PRIMATES Cercopithecidae Rhinopithecus bieti 2. Existing assembly GCF_001698545.1 EN
180 Golden snub-nosed monkey PRIMATES Cercopithecidae Rhinopithecus roxellana 2. Existing assembly GCF_000769185.1 EN
181 Emperor tamarin PRIMATES Cebidae Saguinus imperator 1. Zoonomia GCA_004024885.1 LC
182 Bolivian squirrel monkey PRIMATES Cebidae Saimiri boliviensis 2. Existing assembly GCF_000235385.1 LC
183 Northern Plains gray langur PRIMATES Cercopithecidae Semnopithecus entellus 1. Zoonomia GCA_004025065.1 LC
184 African savanna elephant PROBOSCIDEA Elephantidae Loxodonta Africana 2. Existing assembly GCF_000001905.1 VU
185 Cairo spiny mouse RODENTIA Muridae Acomys cahirinus 1. Zoonomia GCA_004027535.1 LC
186 Gobi jerboa RODENTIA Dipodidae Allactaga bullata 1. Zoonomia GCA_004027895.1 LC
187 Mountain beaver RODENTIA Aplodontiidae Aplodontia rufa 1. Zoonomia GCA_004027875.1 LC
188 Desmarest's hutia RODENTIA Capromyidae Capromys pilorides 1. Zoonomia GCA_004027915.1 LC
189 North American beaver RODENTIA Castoridae Castor canadensis 1. Zoonomia GCA_004027675.1 LC
190 Brazilian guinea pig RODENTIA Caviidae Cavia aperea 2. Existing assembly GCA_000688575.1 LC
191 Domestic guinea pig RODENTIA Caviidae Cavia porcellus 2. Existing assembly GCF_000151735.1 LC
192 Montane guinea pig RODENTIA Caviidae Cavia tschudii 1. Zoonomia GCA_004027695.1 LC
193 Long-tailed chinchilla RODENTIA Chinchillidae Chinchilla lanigera 2. Existing assembly GCF_000276665.1 EN
194 Gambian pouched rat RODENTIA Nesomyidae Cricetomys gambianus 1. Zoonomia GCA_004027575.1 LC
195 Chinese hamster RODENTIA Nesomyidae Cricetulus griseus 2. Existing assembly GCA_900186095.1 LC
196 Common gundi RODENTIA Ctenodactylidae Ctenodactylus gundi 1. Zoonomia GCA_004027205.1 LC
197 Social tuco-tuco RODENTIA Ctenomyidae Ctenomys sociabilis 1. Zoonomia GCA_004027165.1 CR
198 Lowland paca RODENTIA Cuniculidae Cuniculus paca 1. Zoonomia GCA_004365215.1 LC
199 Central American agouti RODENTIA Dasyproctidae Dasyprocta punctata 1. Zoonomia GCA_004363535.1 LC
200 Pacarana RODENTIA Dinomyidae Dinomys branickii 1. Zoonomia GCA_004027595.1 LC
201 Ord's kangaroo rat RODENTIA Heteromyidae Dipodomys ordii 2. Existing assembly GCF_000151885.1 LC
202 Stephen's kangaroo rat RODENTIA Heteromyidae Dipodomys stephensi 1. Zoonomia GCA_004024685.1 VU
203 Patagonian mara RODENTIA Caviidae Dolichotis patagonum 1. Zoonomia GCA_004027295.1 NT
204 Transcaucasian mole vole RODENTIA Cricetidae Ellobius lutescens 2. Existing assembly GCA_001685075.1 LC
205 Northern mole vole RODENTIA Cricetidae Ellobius talpinus 2. Existing assembly GCA_001685095.1 LC
206 Damara mole-rat RODENTIA Bathyergidae Fukomys damarensis 2. Existing assembly GCF_000743615.1 LC
207 Edible dormouse RODENTIA Gliridae Glis glis 1. Zoonomia GCA_004027185.1 LC
208 Woodland doormouse RODENTIA Gliridae Graphiurus murinus 1. Zoonomia GCA_004027655.1 LC
209 Naked mole-rat RODENTIA Bathyergidae Heterocephalus glaber 2. Existing assembly GCF_000247695.1 LC
210 Capybara RODENTIA Caviidae Hydrochoerus hydrochaeris 1. Zoonomia GCA_004027455.1 LC
211 Northern crested porcupine RODENTIA Hystricidae Hystrix cristata 1. Zoonomia GCA_004026905.1 LC
212 Thirteen-lined ground squirrel RODENTIA Sciuridae Ictidomys tridecemlineatus 2. Existing assembly GCF_000236235.1 LC
213 Lesser egyptian jerboa RODENTIA Dipodidae Jaculus jaculus 2. Existing assembly GCF_000280705.1 LC
214 Alpine marmot RODENTIA Sciuridae Marmota marmota 2. Existing assembly GCF_001458135.1 LC
215 Mongolian jird RODENTIA Muridae Meriones unguiculatus 1. Zoonomia GCA_004026785.1 LC
216 Golden hamster RODENTIA Cricetidae Mesocricetus auratus 2. Existing assembly GCF_000349665.1 VU
217 Prairie vole RODENTIA Cricetidae Microtus ochrogaster 2. Existing assembly GCF_000317375.1 LC
218 Ryukyu mouse RODENTIA Muridae Mus caroli 2. Existing assembly GCA_900094665.2 LC
219 House mouse RODENTIA Muridae Mus musculus 2. Existing assembly GCF_000001635.26 LC
220 Shrew mouse RODENTIA Muridae Mus pahari 2. Existing assembly GCA_900095145.2 LC
221 Western wild mouse RODENTIA Muridae Mus spretus 2. Existing assembly GCA_001624865.1 LC
222 Hazel dormouse RODENTIA Gliridae Muscardinus avellanarius 1. Zoonomia GCA_004027005.1 LC
223 Coypu RODENTIA Myocastoridae Myocastor coypus 1. Zoonomia GCA_004027025.1 LC
224 Upper galilee mountains blind mole rat RODENTIA Spalacidae Nannospalax galili 2. Existing assembly GCF_000622305.1 DD
225 Degu RODENTIA Octodontidae Octodon degus 2. Existing assembly GCF_000260255.1 LC
226 Muskrat RODENTIA Cricetidae Ondatra zibethicus 1. Zoonomia GCA_004026605.1 LC
227 Scorpion mouse RODENTIA Cricetidae Onychomys torridus 1. Zoonomia GCA_004026725.1 LC
228 Pacific pocket mouse RODENTIA Heteromyidae Perognathus longimembris pacificus 1. Zoonomia GCA_004363475.1 LC
229 Prairie deer mouse RODENTIA Cricetidae Peromyscus maniculatus 2. Existing assembly GCF_000500345.1 LC
230 Dassie rat RODENTIA Petromuridae Petromus typicus 1. Zoonomia GCA_004026965.1 LC
231 Fat sand rat RODENTIA Muridae Psammomys obesus 2. Existing assembly GCA_002215935.1 LC
232 Norway rat RODENTIA Muridae Rattus norvegicus 2. Existing assembly GCF_000001895.5 LC
233 Hispid cotton rat RODENTIA Cricetidae Sigmodon hispidus 1. Zoonomia GCA_004025045.1 LC
234 Daurian ground squirrel RODENTIA Sciuridae Spermophilus dauricus 2. Existing assembly GCA_002406435.1 LC
235 Greater cane rat RODENTIA Thryonomyidae Thryonomys swinderianus 1. Zoonomia GCA_004025085.1 LC
236 Cape ground squirrel RODENTIA Sciuridae Xerus inauris 1. Zoonomia GCA_004024805.1 LC
237 Meadow jumping mouse RODENTIA Dipodidae Zapus hudsonius 1. Zoonomia GCA_004024765.1 LC
238 Northern tree shrew SCANDENTIA Tupaiidae Tupaia belangeri chinensis 2. Existing assembly GCF_000334495.1 LC
239 Large treeshrew SCANDENTIA Tupaiidae Tupaia tana 1. Zoonomia GCA_004365275.1 LC
240 Florida manatee SIRENIA Trichechidae Trichechus manatus 2. Existing assembly GCF_000243295.1 EN
241 Aardvark TUBULIDENTATA Orycteropodidae Orycteropus afer 1. Zoonomia GCA_004365145.1 LC

Table 1. Genome assemblies included in the 241-way Conservation track.
Species status:LC = Least Concern; NT = Near threatened; VU = Vulnerable; EN = Endangered; CR = Critically endangered

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. 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
UCSC GenesHuman
Ensembl Genes v104Brazilian guinea pig, gibbon
RefSeq GenesAngolan colobus, Balaenoptera acutorostrata, Bison bison, Black flying-fox, Brandt's myotis (bat), Bushbaby, Camelus bactrianus, Camelus ferus, Canis lupus familiaris, Cape elephant shrew, Capra hircus, Cavia porcellus, Ceratotherium simum, Cercocebus atys, Chinchilla, Chinese tree shrew, Chlorocebus sabaeus, Condylura cristata, Damara mole rat, Dasypus novemcinctus, David's myotis (bat), Delphinapterus leucas, Echinops telfairi, Enhydra lutris, Eptesicus fuscus, Equus asinus, Equus przewalskii, Erinaceus europaeus, Felis catus, Heterocephalus glaber, Jaculus jaculus, Kangaroo rat, Killer whale, Leptonychotes weddellii, Lipotes vexillifer, Loxodonta africana, Macaca fascicularis, Macaca nemestrina, Mandrillus leucophaeus, Manis javanica, Marmota marmota, Mesocricetus auratus, Microbat, Miniopterus natalensis, Mus musculus, Nannospalax galili, Ochotona princeps, Octodon degus, Oryctolagus cuniculus, Pacific walrus, Pan paniscus, Panthera tigris, Peromyscus maniculatus, Prairie vole, Propithecus coquereli, Pteropus vampyrus, Puma concolor, Rattus norvegicus, Rhinopithecus bieti, Shrew, Squirrel monkey, Squirrel, Sus scrofa, Trichechus manatus, Ursus maritimus, White-faced sapajou, Wild yak
no annotationAcinonyx jubatus, Acomys cahirinus, Ailuropoda melanoleuca, Ailurus fulgens, Allactaga bullata, Alouatta palliata, Ammotragus lervia, Anoura caudifer, Antilocapra americana, Aotus nancymaae, Aplodontia rufa, Artibeus jamaicensis, Ateles geoffroyi, Balaenoptera bonaerensis, Beatragus hunteri, Bos indicus, Bos taurus, Bubalus bubalis, Callicebus donacophilus, Callithrix jacchus, Camelus dromedarius, Canis lupus, Capra aegagrus, Capromys pilorides, Carollia perspicillata, Castor canadensis, Catagonus wagneri, Cavia tschudii, Cebus albifrons, Ceratotherium simum cottoni, Cercopithecus neglectus, Chaetophractus vellerosus, Cheirogaleus medius, Choloepus didactylus, Choloepus hoffmanni, Chrysochloris asiatica, Craseonycteris thonglongyai, Cricetomys gambianus, Cricetulus griseus, Crocidura indochinensis, Cryptoprocta ferox, Ctenodactylus gundi, Ctenomys sociabilis, Cuniculus paca, Dasyprocta punctata, Daubentonia madagascariensis, Desmodus rotundus, Dicerorhinus sumatrensis, Diceros bicornis, Dinomys branickii, Dipodomys stephensi, Dolichotis patagonum, Elaphurus davidianus, Ellobius lutescens, Ellobius talpinus, Equus caballus, Erythrocebus patas, Eschrichtius robustus, Eubalaena japonica, Eulemur flavifrons, Eulemur fulvus, Felis nigripes, Galeopterus variegatus, Giraffa tippelskirchi, Glis glis, Gorilla gorilla, Graphiurus murinus, Helogale parvula, Hemitragus hylocrius, Heterohyrax brucei, Hippopotamus amphibius, Hipposideros armiger, Hipposideros galeritus, Hyaena hyaena, Hydrochoerus hydrochaeris, Hystrix cristata, Indri indri, Inia geoffrensis, Kogia breviceps, Lasiurus borealis, Lemur catta, Lepus americanus, Lycaon pictus, Macaca mulatta, Macroglossus sobrinus, Manis pentadactyla, Megaderma lyra, Mellivora capensis, Meriones unguiculatus, Mesoplodon bidens, Microcebus murinus, Microgale talazaci, Micronycteris hirsuta, Miniopterus schreibersii, Mirounga angustirostris, Mirza coquereli, Monodon monoceros, Mormoops blainvillei, Moschus moschiferus, Mungos mungo, Murina feae, Mus caroli, Mus pahari, Mus spretus, Muscardinus avellanarius, Mustela putorius, Myocastor coypus, Myotis myotis, Myrmecophaga tridactyla, Nasalis larvatus, Neomonachus schauinslandi, Neophocaena asiaeorientalis, Noctilio leporinus, Nycticebus coucang, Odocoileus virginianus, Okapia johnstoni, Ondatra zibethicus, Onychomys torridus, Orycteropus afer, Ovis aries, Ovis canadensis, Pan troglodytes, Panthera onca, Panthera pardus, Pantholops hodgsonii, Papio anubis, Paradoxurus hermaphroditus
Table 2. Gene tracks used for codon translation.

Methods

The Zoonomia alignment was composed of two sets of mammalian genomes: newly assembled DISCOVAR assemblies and GenBank assemblies. The DISCOVAR genomes were masked with RepeatMasker (commit 2d947604), using Repbase version 20170127 as the repeat library and CrossMatch as the alignment engine. The pipeline used is available at repeatMaskerPipeline (commit a6ad966). The guide-tree topology was taken from the TimeTree database (using release current in October 2018), and the branch lengths were estimated using the least-squares-fit mode of PHYLIP, version 3.695. The distance matrix used was largely based on distances from the 4d site trees from the UCSC browser. To add those species not present in the UCSC tree, approximate distances estimated by Mash (commit 541971b) to the closest UCSC species were added to the distance between the two closest UCSC species. We used the HAL package (commit 68db41d) produce the HAL file.

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 241-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 ( 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).

References

Zoonomia:

Zoonomia Consortium.. A comparative genomics multitool for scientific discovery and conservation. Nature. 2020 Nov;587(7833):240-245. PMID: 33177664; PMC: PMC7759459; DOI: 10.1038/s41586-020-2876-6

Cactus:

Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J et al. Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature. 2020 Nov;587(7833):246-251. PMID: 33177663; PMC: PMC7673649; DOI: 10.1038/s41586-020-2871-y

Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011 Sep;21(9):1512-28. PMID: 21665927; PMC: PMC3166836; DOI: 10.1101/gr.123356.111

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

PhyloP:

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