mm39 Mouse: Multiz Alignments of 35 Vertebrates
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Data last updated at UCSC: 2020-12-20


This track shows multiple alignments of 35 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package.

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 conservation measurements were created using the phastCons package from Adam Siepel at Cold Spring Harbor Laboratory.

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

See also: lastz parameters and other details for the chaining minimum score and gap parameters used in these alignments.

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.

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).

MouseMus musculus Jun. 2020 (GRCm39/mm39)Jun. 2020 (GRCm39/mm39)reference species
BeaverCastor canadensis Feb. 2017 (C.can genome v1.0/casCan1)Feb. 2017 (C.can genome v1.0/casCan1)reciprocal best
BonoboPan paniscus May 2020 (Mhudiblu_PPA_v0/panPan3)May 2020 (Mhudiblu_PPA_v0/panPan3)syntenic net
BushbabyOtolemur garnettii Mar. 2011 (Broad/otoGar3)Mar. 2011 (Broad/otoGar3)reciprocal best
ChickenGallus gallus Mar. 2018 (GRCg6a/galGal6)Mar. 2018 (GRCg6a/galGal6)maf net
ChimpPan troglodytes Jan. 2018 (Clint_PTRv2/panTro6)Jan. 2018 (Clint_PTRv2/panTro6)syntenic net
Chinese hamsterCricetulus griseus Jun. 2020 (GCF_0003668045.3 CriGri-PICRH-1.0)Jun. 2020 (GCF_0003668045.3 CriGri-PICRH-1.0)syntenic net
Chinese pangolinManis pentadactyla Aug 2014 (M_pentadactyla-1.1.1/manPen1)Aug 2014 (M_pentadactyla-1.1.1/manPen1)reciprocal best
CowBos taurus Apr. 2018 (ARS-UCD1.2/bosTau9)Apr. 2018 (ARS-UCD1.2/bosTau9)reciprocal best
DogCanis lupus familiaris Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)Mar. 2020 (UU_Cfam_GSD_1.0/canFam4)syntenic net
DolphinTursiops truncatus Oct. 2011 (Baylor Ttru_1.4/turTru2)Oct. 2011 (Baylor Ttru_1.4/turTru2)reciprocal best
ElephantLoxodonta africana Jul. 2009 (Broad/loxAfr3)Jul. 2009 (Broad/loxAfr3)reciprocal best
GorillaGorilla gorilla gorilla Aug. 2019 (Kamilah_GGO_v0/gorGor6)Aug. 2019 (Kamilah_GGO_v0/gorGor6)syntenic net
Guinea pigCavia porcellus Feb. 2008 (Broad/cavPor3)Feb. 2008 (Broad/cavPor3)syntenic net
Hawaiian monk sealNeomonachus schauinslandi Jun. 2017 (ASM220157v1/neoSch1)Jun. 2017 (ASM220157v1/neoSch1)syntenic net
HedgehogErinaceus europaeus May 2012 (EriEur2.0/eriEur2)May 2012 (EriEur2.0/eriEur2)reciprocal best
HorseEquus caballus Jan. 2018 (EquCab3.0/equCab3)Jan. 2018 (EquCab3.0/equCab3)syntenic net
HumanHomo sapiens Dec. 2013 (GRCh38/hg38)Dec. 2013 (GRCh38/hg38)syntenic net
LampreyPetromyzon marinus Dec. 2017 (Pmar_germline 1.0/petMar3)Dec. 2017 (Pmar_germline 1.0/petMar3)maf net
Malayan flying lemurGaleopterus variegatus Jun. 2014 (G_variegatus-3.0.2/galVar1)Jun. 2014 (G_variegatus-3.0.2/galVar1)maf net
MarmosetCallithrix jacchus May 2020 (Callithrix_jacchus_cj1700_1.1/calJac4)May 2020 (Callithrix_jacchus_cj1700_1.1/calJac4)syntenic net
OpossumMonodelphis domestica Oct. 2006 (Broad/monDom5)Oct. 2006 (Broad/monDom5)maf net
PigSus scrofa Aug. 2011 (SGSC Sscrofa10.2/susScr3)Aug. 2011 (SGSC Sscrofa10.2/susScr3)reciprocal best
PikaOchotona princeps May 2012 (OchPri3.0/ochPri3)May 2012 (OchPri3.0/ochPri3)reciprocal best
RabbitOryctolagus cuniculus Apr. 2009 (Broad/oryCun2)Apr. 2009 (Broad/oryCun2)reciprocal best
RatRattus norvegicus Jul. 2014 (RGSC 6.0/rn6)Jul. 2014 (RGSC 6.0/rn6)syntenic net
RhesusMacaca mulatta Feb. 2019 (Mmul_10/rheMac10)Feb. 2019 (Mmul_10/rheMac10)syntenic net
SheepOvis aries Nov. 2015 (Oar_v4.0/oviAri4)Nov. 2015 (Oar_v4.0/oviAri4)syntenic net
ShrewSorex araneus Aug. 2008 (Broad/sorAra2)Aug. 2008 (Broad/sorAra2)reciprocal best
SquirrelSpermophilus tridecemlineatus Nov. 2011 (Broad/speTri2)Nov. 2011 (Broad/speTri2)reciprocal best
TarsierTarsius syrichta Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)Sep. 2013 (Tarsius_syrichta-2.0.1/tarSyr2)reciprocal best
TenrecEchinops telfairi Nov. 2012 (Broad/echTel2)Nov. 2012 (Broad/echTel2)reciprocal best
Tree shrewTupaia belangeri Dec. 2006 (Broad/tupBel1)Dec. 2006 (Broad/tupBel1)reciprocal best
X. tropicalisXenopus tropicalis Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)Jul. 2016 (Xenopus_tropicalis_v9.1/xenTro9)maf net
ZebrafishDanio rerio May 2017 (GRCz11/danRer11)May 2017 (GRCz11/danRer11)maf net

Table 1. Genome assemblies included in the 35-way Conservation track.
* Data download only, browser not available.

Display Conventions and Configuration

The track configuration options allow the user to display either the vertebrate or placental mammal conservation scores, or both simultaneously. 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 mouse 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 mouse 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 mouse 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 mouse sequence at those alignment positions relative to the longest non-mouse 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
Known Geneshuman
Ensembl Genestree shrew, opossum
NCBI RefSeqbeaver, bonobo, bushbaby, chicken, Chinese hamster, chimp, cow, elephant, gorilla, guinea pig, hawaiian monk seal, hedgehog, horse, malayan flying lemur, marmoset, mouse, pig, pika, rabbit, rat, rhesus, sheep, shrew, squirrel, tarsier, tenrec, X. tropicalis, zebrafish
Xeno RefGeneChinese pangolin, dog, dolphin, lamprey
Table 2. Gene tracks used for codon translation.


Pairwise alignments with the mouse 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. For more information about the chaining and netting process and parameters for each species, see the description pages for the Chain and Net tracks.

An additional filtering step was introduced in the generation of the 35-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: the pairwise alignments of high-quality mammalian sequences (placental and marsupial) were filtered based on synteny; those for 2X mammalian genomes were filtered to retain only alignments of best quality in both the target and query ("reciprocal best").

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.

Conservation scoring was performed using the PhastCons package (A. Siepel), which computes conservation based on a two-state phylogenetic hidden Markov model (HMM). PhastCons measurements 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 vertebrate tree model for this track was generated using the phyloFit program from the phastCons package (REV model, EM algorithm, medium precision) using multiple alignments of 4-fold degenerate sites extracted from the 28-way human(hg18) alignment (msa_view). The 4d sites were derived from the Oct 2005 Gencode Reference Gene set, which was filtered to select single-coverage long transcripts. The phastCons parameters used for the conservation measurement were: expected-length=45, target-coverage=.3 and rho=.31

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, note that 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.

PhastCons currently treats alignment gaps as missing data, which sometimes has the effect of producing undesirably high conservation scores in gappy regions of the alignment. We are looking at several possible ways of improving the handling of alignment gaps.

Data Access

You can access this data in the Table Browser for position or identifier based queries in multiple formats. Downloads for data in this track are available in the following locations:


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, phyloFit, tree_doctor, msa_view by Adam Siepel while at UCSC, now at Cold Spring Harbor Laboratory
  • 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 and phastCons:

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

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

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

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