Conservation Track Settings
Vertebrate Multiz Alignment & Conservation (77 Species)   (All Comparative Genomics tracks)

Maximum display mode:       Reset to defaults   
Select views (Help):
Multiz Alignments ▾       Basewise Conservation (phyloP) ▾       Element Conservation (phastCons) ▾       Conserved Elements ▾      
Multiz Alignments Configuration

Species selection:  + - default

  Birds  + -

japanese quail
golden eagle
bald eagle
crested ibis
emperor penguin
peregrine falcon
saker falcon
adelie penguin
little egret
mallard duck
dalmatian pelican
northern fulmar
red-legged seriema
cuckoo roller
white-tailed eagle
american flamingo
red-throated loon
crowned crain
white-tailed tropicbird
red crested turaco
great cormorant
barn owl
common cuckoo
rock pigeon
houbara bustard
brown roatelo
yellow-throated sandgrouse
northern carmine bee-eater
bar tailed trogon
speckled mousebird
american crow
rhinoceros hornbill
tibetan ground jay
hooded crow
anna's hummingbird
collared flycatcher
medium ground finch
white-throated sparrow
scarlet macaw
downy woodpecker
zebra finch
white throated tinamou

  Reptiles  + -

chinese alligator
american alligator
chinese softshell turtle
spiny softshell turtle
burmese python
garter snake
painted turtle
green seaturtle

  Vertebrate  + -

japanese eel
nile tilapia
zebra mbuna
arctic lamprey
x. tropicalis
african clawed frog
tibetan frog

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
Select subtracks by clade:
  Clade Vertebrate  All species 
List subtracks: only selected/visible    all  
 Cons 77 Verts  77 vertebrates Basewise Conservation by PhyloP   Data format 
 Cons 77 Verts  77 vertebrates conservation by PhastCons   Data format 
 77 Vert. El  77 vertebrates Conserved Elements   Data format 
 Multiz Align  Multiz Alignments of 77 Vertebrates   Data format 


This track shows multiple alignments of 77 vertebrate species: 55 birds, 10 reptiles (alligator, snake, frog) and 12 other species (fish, human, mouse, lamprey) and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 77 species. The multiple alignments were generated using multiz and other tools in the UCSC/Penn State Bioinformatics comparative genomics alignment pipeline. Conserved elements identified by phastCons are also displayed in this track.

PhastCons (which has been used in previous Conservation tracks) is a hidden Markov model-based method that estimates the probability that each nucleotide belongs to a conserved element, based on the multiple alignment. It considers not just each individual alignment column, but also its flanking columns. By contrast, phyloP separately measures conservation at individual columns, ignoring the effects of their neighbors. As a consequence, the phyloP plots have a less smooth appearance than the phastCons plots, with more "texture" at individual sites. The two methods have different strengths and weaknesses. PhastCons is sensitive to "runs" of conserved sites, and is therefore effective for picking out conserved elements. PhyloP, on the other hand, is more appropriate for evaluating signatures of selection at particular nucleotides or classes of nucleotides (e.g., third codon positions, or first positions of miRNA target sites).

Another important difference is that phyloP can measure acceleration (faster evolution than expected under neutral drift) as well as conservation (slower than expected evolution). In the phyloP plots, sites predicted to be conserved are assigned positive scores (and shown in blue), while sites predicted to be fast-evolving are assigned negative scores (and shown in red). The absolute values of the scores represent -log p-values under a null hypothesis of neutral evolution. The phastCons scores, by contrast, represent probabilities of negative selection and range between 0 and 1.

Both phastCons and phyloP treat alignment gaps and unaligned nucleotides as missing data.

See also: lastz parameters and other details, and chain minimum score and gap parameters used in these alignments.

Missing sequence in the assemblies is highlighted in the track display by regions of yellow when zoomed out and Ns displayed at base level (see Gap Annotation, below).

OrganismSpeciesAssembly namebrowser or
NCBI source
alignment type
ChickenGallus gallus Mar. 2018 (GRCg6a/galGal6) Mar. 2018 (GRCg6a/galGal6) reference
Adelie penguinPygoscelis adeliae Jun 2014 (ASM69910v1/pygAde1) Jun 2014 (ASM69910v1/pygAde1) syntenic
African clawed frogXenopus laevis Aug. 2016 (Xenopus_laevis_v2/xenLae2) Aug. 2016 (Xenopus_laevis_v2/xenLae2) net
American alligatorAlligator mississippiensis Aug. 2012 (allMis0.2/allMis1) Aug. 2012 (allMis0.2/allMis1) reciprocal best
American crowCorvus brachyrhynchos Jun 2014 (ASM69197v1/corBra1) Jun 2014 (ASM69197v1/corBra1) syntenic
American flamingoPhoenicopterus ruber ruber May 2014 (ASM68726v1/phoRub1) May 2014 (ASM68726v1/phoRub1) reciprocal best
Anna's hummingbirdCalypte anna Jun 2014 (ASM69908v1/calAnn1) Jun 2014 (ASM69908v1/calAnn1) syntenic
Arctic lampreyLethenteron camtschaticum Sep 2013 (LetJap1.0/letCam1) Sep 2013 (LetJap1.0/letCam1) net
Bald eagleHaliaeetus leucocephalus Aug 2014 (Haliaeetus_leucocephalus-4.0/halLeu1) Aug 2014 (Haliaeetus_leucocephalus-4.0/halLeu1) syntenic
Bar tailed trogonApaloderma vittatum 16 Jun 2014 (ASM70340v1/apaVit1) 16 Jun 2014 (ASM70340v1/apaVit1) reciprocal best
Barn owlTyto alba May 2014 (ASM68720v1/tytAlb1) May 2014 (ASM68720v1/tytAlb1) reciprocal best
Brown roateloMesitornis unicolor Jun 2014 (ASM69576v1/mesUni1) Jun 2014 (ASM69576v1/mesUni1) reciprocal best
BudgerigarMelopsittacus undulatus Sep. 2011 (WUSTL v6.3/melUnd1) Sep. 2011 (WUSTL v6.3/melUnd1) syntenic
Burmese pythonPython bivittatus Sep. 2013 (Python_molurus_bivittatus-5.0.2/pytBiv1) Sep. 2013 (Python_molurus_bivittatus-5.0.2/pytBiv1) net
CanarySerinus canaria 15 Jan-2014 (SCA1/serCan1) 15 Jan-2014 (SCA1/serCan1) syntenic
Chinese alligatorAlligator sinensis 29 Aug 2013 (ASM45574v1/allSin1) 29 Aug 2013 (ASM45574v1/allSin1) reciprocal best
Chinese softshell turtlePelodiscus sinensis Oct 2011 (PelSin_1.0/pelSin1) Oct 2011 (PelSin_1.0/pelSin1) reciprocal best
Chuck-will's-widowCaprimulgus carolinensis Jun 2014 (ASM70074v1/capCar1) Jun 2014 (ASM70074v1/capCar1) reciprocal best
Collared flycatcherFicedula albicollis Jun 2013 (FicAlb1.5/ficAlb2) Jun 2013 (FicAlb1.5/ficAlb2) syntenic
Common cuckooCuculus canorus Jun 2014 (ASM70932v1/cucCan1) Jun 2014 (ASM70932v1/cucCan1) reciprocal best
Crested ibisNipponia nippon Jun 2014 (ASM70822v1/nipNip1) Jun 2014 (ASM70822v1/nipNip1) syntenic
Crowned crainBalearica pavonina gibbericeps Jun 2014 (ASM70989v1/balPav1) Jun 2014 (ASM70989v1/balPav1) reciprocal best
Cuckoo rollerLeptosomus discolor May 2014 (ASM69178v1/lepDis1) May 2014 (ASM69178v1/lepDis1) reciprocal best
Dalmatian pelicanPelecanus crispus May 2014 (ASM68737v1/pelCri1) May 2014 (ASM68737v1/pelCri1) reciprocal best
Downy woodpeckerPicoides pubescens Jun 2014 (ASM69900v1/picPub1) Jun 2014 (ASM69900v1/picPub1) reciprocal best
Emperor penguinAptenodytes forsteri 06 Jun 2014 (ASM69914v1/aptFor1) 06 Jun 2014 (ASM69914v1/aptFor1) syntenic
FuguTakifugu rubripes Oct. 2011 (FUGU5/fr3) Oct. 2011 (FUGU5/fr3) net
Garter snakeThamnophis sirtalis Jun. 2015 (Thamnophis_sirtalis-6.0/thaSir1) Jun. 2015 (Thamnophis_sirtalis-6.0/thaSir1) net
Golden eagleAquila chrysaetos canadensis Oct. 2014 (aquChr-1.0.2/aquChr2) Oct. 2014 (aquChr-1.0.2/aquChr2) syntenic
Great cormorantPhalacrocorax carbo Jun 2014 (ASM70892v1/phaCar1) Jun 2014 (ASM70892v1/phaCar1) reciprocal best
Green seaturtleChelonia mydas Mar 2013 (CheMyd_1.0/cheMyd1) Mar 2013 (CheMyd_1.0/cheMyd1) reciprocal best
HoatzinOpisthocomus hoazin May 2014 (ASM69207v1/opiHoa1) May 2014 (ASM69207v1/opiHoa1) reciprocal best
Hooded crowCorvus cornix cornix Aug 2014 (Hooded_Crow_genome/corCor1) Aug 2014 (Hooded_Crow_genome/corCor1) syntenic
Houbara bustardChlamydotis undulata macqueenii Jun 2014 (ASM69519v1/chlUnd1) Jun 2014 (ASM69519v1/chlUnd1) reciprocal best
HumanHomo sapiens Dec. 2013 (GRCh38/hg38) Dec. 2013 (GRCh38/hg38) net
Japanese eelAnguilla japonica 18 Mar-2014 (japanese_eel_genome_v1 25_oct_2011_japonica_c401b400k25m200 sspacepremiumk3a02n24 18 Mar-2014 (japanese_eel_genome_v1 25_oct_2011_japonica_c401b400k25m200 sspacepremiumk3a02n24 net
Japanese quailCoturnix japonica Mar. 2016 (Coturnix japonica 2.0/cotJap2) Mar. 2016 (Coturnix japonica 2.0/cotJap2) reciprocal best
KilldeerCharadrius vociferus Aug 2014 (ASM70802v2/chaVoc2) Aug 2014 (ASM70802v2/chaVoc2) syntenic
LampreyPetromyzon marinus Dec. 2017 (Pmar_germline 1.0/petMar3) Dec. 2017 (Pmar_germline 1.0/petMar3) net
Little egretEgretta garzetta May 2014 (ASM68718v1/egrGar1) May 2014 (ASM68718v1/egrGar1) reciprocal best
LizardAnolis carolinensis May 2010 (Broad AnoCar2.0/anoCar2) May 2010 (Broad AnoCar2.0/anoCar2) net
Mallard duckAnas platyrhynchos Apr 2013 (BGI_duck_1.0/anaPla1) Apr 2013 (BGI_duck_1.0/anaPla1) reciprocal best
MedakaOryzias latipes Oct. 2005 (NIG/UT MEDAKA1/oryLat2) Oct. 2005 (NIG/UT MEDAKA1/oryLat2) net
Medium ground finchGeospiza fortis Apr. 2012 (GeoFor_1.0/geoFor1) Apr. 2012 (GeoFor_1.0/geoFor1) syntenic
MouseMus musculus Dec. 2011 (GRCm38/mm10) Dec. 2011 (GRCm38/mm10) net
Nile tilapiaOreochromis niloticus Nov. 2016 (ASM185804v2/oreNil3) Nov. 2016 (ASM185804v2/oreNil3) net
Northern carmine bee-eaterMerops nubicus May 2014 (ASM69184v1/merNub1) May 2014 (ASM69184v1/merNub1) reciprocal best
Northern fulmarFulmarus glacialis May 2014 (ASM69083v1/fulGla1) May 2014 (ASM69083v1/fulGla1) reciprocal best
OstrichStruthio camelus australis 06 Jun-2014 (ASM69896v1/strCam1) 06 Jun-2014 (ASM69896v1/strCam1) reciprocal best
Painted turtleChrysemys picta bellii Mar. 2014 (v3.0.3/chrPic2) Mar. 2014 (v3.0.3/chrPic2) syntenic
ParrotAmazona vittata Jan. 2013 (AV1/amaVit1) Jan. 2013 (AV1/amaVit1) reciprocal best
Peregrine falconFalco peregrinus Feb 2013 (F_peregrinus_v1.0/falPer1) Feb 2013 (F_peregrinus_v1.0/falPer1) syntenic
Red crested turacoTauraco erythrolophus Jun 2014 (ASM70936v1/tauEry1) Jun 2014 (ASM70936v1/tauEry1) reciprocal best
Red-legged seriemaCariama cristata May 2014 (ASM69053v1/carCri1) May 2014 (ASM69053v1/carCri1) reciprocal best
Red-throated loonGavia stellata May 2014 (ASM69087v1/gavSte1) May 2014 (ASM69087v1/gavSte1) reciprocal best
Rhinoceros hornbillBuceros rhinoceros silvestris Jun 2014 (ASM71030v1/bucRhi1) Jun 2014 (ASM71030v1/bucRhi1) reciprocal best
RiflemanAcanthisitta chloris 27 May 2014 (ASM69581v1/acaChl1) 27 May 2014 (ASM69581v1/acaChl1) reciprocal best
Rock pigeonColumba livia Feb 2013 (Cliv_1.0/colLiv1) Feb 2013 (Cliv_1.0/colLiv1) syntenic
Saker falconFalco cherrug Feb 2013 (F_cherrug_v1.0/falChe1) Feb 2013 (F_cherrug_v1.0/falChe1) syntenic
Scarlet macawAra macao Jun 2013 (SMACv1.1/araMac1) Jun 2013 (SMACv1.1/araMac1) reciprocal best
Speckled mousebirdColius striatus May 2014 (ASM69071v1/colStr1) May 2014 (ASM69071v1/colStr1) reciprocal best
Spiny softshell turtleApalone spinifera May 2013 (ASM38561v1/apaSpi1) May 2013 (ASM38561v1/apaSpi1) reciprocal best
SticklebackGasterosteus aculeatus Feb. 2006 (Broad/gasAcu1) Feb. 2006 (Broad/gasAcu1) net
SunbitternEurypyga helias May 2014 (ASM69077v1/eurHel1) May 2014 (ASM69077v1/eurHel1) reciprocal best
TetraodonTetraodon nigroviridis Mar. 2007 (Genoscope 8.0/tetNig2) Mar. 2007 (Genoscope 8.0/tetNig2) net
Tibetan frogNanorana parkeri Mar. 2015 (BGI_ZX_2015/nanPar1) Mar. 2015 (BGI_ZX_2015/nanPar1) net
Tibetan ground jayPseudopodoces humilis Jan 2013 (PseHum1.0/pseHum1) Jan 2013 (PseHum1.0/pseHum1) syntenic
TurkeyMeleagris gallopavo Nov. 2014 (Turkey_5.0/melGal5) Nov. 2014 (Turkey_5.0/melGal5) reciprocal best
White throated tinamouTinamus guttatus Aug 2014 (ASM70537v2/tinGut2) Aug 2014 (ASM70537v2/tinGut2) reciprocal best
White-tailed eagleHaliaeetus albicilla May 2014 (ASM69140v1/halAlb1) May 2014 (ASM69140v1/halAlb1) reciprocal best
White-tailed tropicbirdPhaethon lepturus May 2014 (ASM68728v1/phaLep1) May 2014 (ASM68728v1/phaLep1) reciprocal best
White-throated sparrowZonotrichia albicollis Apr 2013 (ASM38545v1/zonAlb1) Apr 2013 (ASM38545v1/zonAlb1) syntenic
X. tropicalisXenopus tropicalis Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9) net
Yellow-throated sandgrousePterocles gutturalis Jun 2014 (ASM69924v1/pteGut1) Jun 2014 (ASM69924v1/pteGut1) reciprocal best
Zebra finchTaeniopygia guttata Feb. 2013 (WashU taeGut324/taeGut2) Feb. 2013 (WashU taeGut324/taeGut2) syntenic
Zebra mbunaMaylandia zebra Mar 2012 (MetZeb1.1/mayZeb1) Mar 2012 (MetZeb1.1/mayZeb1) net
ZebrafishDanio rerio May 2017 (GRCz11/danRer11) May 2017 (GRCz11/danRer11) net

Table 1. Genome assemblies included in the 77-way Conservation track.

Downloads for data in this track are available:

Display Conventions and Configuration

The track configuration options allow the user to display the three different sets of alignments: all, birds, reptiles or vertebrate, individually or all simultaneously. In full and pack display modes, conservation scores are displayed as a wiggle track (histogram) in which the height reflects the value of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options.

Pairwise alignments of each species to the chicken genome are displayed below the conservation histogram as a grayscale density plot (in pack mode) or as a wiggle (in full mode) that indicates alignment quality. In dense display mode, conservation is shown in grayscale using darker values to indicate higher levels of overall conservation as scored by phastCons.

Checkboxes on the track configuration page allow selection of the species to include in the pairwise display. Configuration buttons are available to select all of the species (Set all), deselect all of the species (Clear all), or use the default settings (Set defaults). Note that excluding species from the pairwise display does not alter the 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 chicken 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 chicken 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 chicken sequence at those alignment positions relative to the longest non-chicken 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, depending on the species chosen (Table 2).

Gene TrackSpecies
NCBI RefSeq GenesChicken, Japanese quail, Turkey, Medium ground finch, Zebra finch, Budgerigar, American alligator
Ensembl Genes v92Mallard duck, Chinese softshell turtle
Xeno RefGeneGolden eagle, Painted turtle
no annotationsall others
Table 2. Gene tracks used for codon translation.


Pairwise alignments with the chicken genome were generated for each species using lastz from repeat-masked genomic sequence. Pairwise alignments were then linked into chains using a dynamic programming algorithm that finds maximally scoring chains of gapless subsections of the alignments organized in a kd-tree. Please note the specific parametersfor the alignments. High-scoring chains were then placed along the genome, with gaps filled by lower-scoring chains, to produce an alignment net. For more information about the chaining and netting process for each species, see the description pages for the Chain and Net tracks.

An additional filtering step was introduced in the generation of the 77-way conservation track to reduce the number of paralogs and pseudogenes from the high-quality assemblies and the suspect alignments from the low-quality assemblies: some of the pairwise alignments were filtered based on synteny; and others were filtered to retain only alignments of best quality in both the target and query ("reciprocal best"). Note the indication in the table above for this filtering option.

The resulting best-in-genome pairwise alignments were progressively aligned using multiz/autoMZ, following the tree topology diagrammed above, to produce multiple alignments. The multiple alignments were post-processed to add annotations indicating alignment gaps, genomic breaks, and base quality of the component sequences. The annotated multiple alignments, in MAF format, are available for bulk download. An alignment summary table containing an entry for each alignment block in each species was generated to improve track display performance at large scales. Framing tables were constructed to enable visualization of codons in the multiple alignment display.

Phylogenetic Tree Model

Both phastCons and phyloP are phylogenetic methods that rely on a tree model containing the tree topology, branch lengths representing evolutionary distance at neutrally evolving sites, the background distribution of nucleotides, and a substitution rate matrix. The all species tree model for this track was generated using the phyloFit program from the PHAST package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 77-way alignment (msa_view). The 4d sites were derived from the NCBI RefSeq gene set, filtered to select single-coverage long transcripts.

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

PhastCons Conservation

The phastCons program computes conservation scores based on a phylo-HMM, a type of probabilistic model that describes both the process of DNA substitution at each site in a genome and the way this process changes from one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for conserved regions and a state for non-conserved regions. The value plotted at each site is the posterior probability that the corresponding alignment column was "generated" by the conserved state of the phylo-HMM. These scores reflect the phylogeny (including branch lengths) of the species in question, a continuous-time Markov model of the nucleotide substitution process, and a tendency for conservation levels to be autocorrelated along the genome (i.e., to be similar at adjacent sites). The general reversible (REV) substitution model was used. Unlike many conservation-scoring programs, phastCons does not rely on a sliding window of fixed size; therefore, short highly-conserved regions and long moderately conserved regions can both obtain high scores. More information about phastCons can be found in Siepel et al. 2005.

The phastCons parameters used were: expected-length=45, target-coverage=0.3, rho=0.3.

PhyloP Conservation

The phyloP program supports several different methods for computing p-values of conservation or acceleration, for individual nucleotides or larger elements ( Here it was used to produce separate scores at each base (--wig-scores option), considering all branches of the phylogeny rather than a particular subtree or lineage (i.e., the --subtree option was not used). The scores were computed by performing a likelihood ratio test at each alignment column (--method LRT), and scores for both conservation and acceleration were produced (--mode CONACC).

Conserved Elements

The conserved elements were predicted by running phastCons with the --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the phylo-HMM. Each element is assigned a log-odds score equal to its log probability under the conserved model minus its log probability under the non-conserved model. The "score" field associated with this track contains transformed log-odds scores, taking values between 0 and 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the "name" field and can be seen on the details page or in the browser when the track's display mode is set to "pack" or "full".


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

The phylogenetic tree is based on Murphy et al. (2001) and general consensus in the vertebrate phylogeny community as of March 2007.


Phylo-HMMs, phastCons, and phyloP:

Felsenstein J, Churchill GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996 Jan;13(1):93-104. PMID: 8583911

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21. PMID: 19858363; PMC: PMC2798823

Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. PMID: 16024819; PMC: PMC1182216

Siepel A, Haussler D. Phylogenetic Hidden Markov Models. In: Nielsen R, editor. Statistical Methods in Molecular Evolution. New York: Springer; 2005. pp. 325-351.

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


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


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

Lastz (formerly Blastz):

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

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

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

Phylogenetic Tree:

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