Cons 124 Insects Track Settings
Multiz Alignment & Conservation (124 insects)   (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

  Brachycera  + -

d. simulans
d. sechellia
d. yakuba
d. erecta
d. takahashii
d. elegans
d. eugracilis
d. biarmipes
d. rhopaloa
d. ficusphila
d. suzukii
d. kikkawai
d. ananassae
d. bipectinata
d. pseudoobscura
d. miranda
d. persimilis
d. virilis
d. willistoni
d. grimshawi
d. mojavensis
d. albomicans
m. domestica

  Nematocera  + -

a. gambiae

  Holometabola  + -

t. castaneum
a. mellifera

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  
 Cons 124 insects  124 insects Basewise Conservation by PhyloP   Data format 
 Cons 124 insects  124 insects conservation by PhastCons   Data format 
 124 insects El  124 insects Conserved Elements   Data format 
 Multiz Align  Multiz Alignments of 124 insects   Data format 


This track shows multiple alignments of 124 insects and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package, for all 124 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.

The phylogenetic tree was derived from kmers in common counting between the sequences to obtain a 'distance' matrix, then using the phylip command 'neighbors' operation for the simple neighbor joining algorithm to establish this binary tree. This tree is not necessarily biologically correct, but it does serve as a useful guide tree for the multiz alignment procedure. See also: Phylip distance operations

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
D. melanogasterDrosophila melanogaster Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6) reference
A. albimanusAnopheles albimanus Aug. 2017 (Anop_albi_ALBI9_A_V2) GCA_000349125.2 net
A. aquasalisAnopheles aquasalis Dec. 2017 (A_aquasalis_v1.0) GCA_002846955.1 net
A. arabiensisAnopheles arabiensis Apr. 2013 (Anop_arab_DONG5_A_V1) GCA_000349185.1 net
A. atroparvusAnopheles atroparvus Sep. 2013 (Anop_atro_EBRO_V1) GCA_000473505.1 net
A. christyiAnopheles christyi Apr. 2013 (Anop_chri_ACHKN1017_V1) GCA_000349165.1 net
A. coluzziiAnopheles coluzzii Apr. 2008 (m5) GCA_000150765.1 net
A. cracensAnopheles cracens Apr. 2017 (ASM209184v1) GCA_002091845.1 net
A. culicifaciesAnopheles culicifacies Sep. 2013 (Anop_culi_species_A-37_1_V1) GCA_000473375.1 net
A. darlingiAnopheles darlingi Dec. 2013 (A_darlingi_v1) GCA_000211455.3 net
A. dirusAnopheles dirus Mar. 2013 (Anop_diru_WRAIR2_V1) GCA_000349145.1 net
A. epiroticusAnopheles epiroticus Mar. 2013 (Anop_epir_epiroticus2_V1) GCA_000349105.1 net
A. farautiAnopheles farauti Jan. 2014 (Anop_fara_FAR1_V2) GCA_000473445.2 net
A. farauti_No4Anopheles farauti No. 4 Mar. 2015 (ASM95621v1) GCA_000956215.1 net
A. funestusAnopheles funestus Mar. 2013 (Anop_fune_FUMOZ_V1) GCA_000349085.1 net
A. gambiaeAnopheles gambiae Oct. 2006 (AgamP3/anoGam3) Oct. 2006 (AgamP3/anoGam3) net
A. gambiae_1Anopheles gambiae str. PEST Oct. 2006 (AgamP3) GCF_000005575.2 net
A. koliensisAnopheles koliensis Mar. 2015 (ASM95627v1) GCA_000956275.1 net
A. maculatusAnopheles maculatus Apr. 2017 (ASM209183v1) GCA_002091835.1 net
A. melasAnopheles melas Jan. 2014 (Anop_mela_CM1001059_A_V2) GCA_000473525.2 net
A. melliferaApis mellifera 04 Nov 2010 (Amel_4.5/apiMel4) 04 Nov 2010 (Amel_4.5/apiMel4) net
A. merusAnopheles merus Jan. 2014 (Anop_meru_MAF_V1) GCA_000473845.2 net
A. minimusAnopheles minimus Mar. 2013 (Anop_mini_MINIMUS1_V1) GCA_000349025.1 net
A. niliAnopheles nili Jul. 2013 (Anili1) GCA_000439205.1 net
A. punctulatusAnopheles punctulatus Mar. 2015 (ASM95625v1) GCA_000956255.1 net
A. quadriannulatusAnopheles quadriannulatus Mar. 2013 (Anop_quad_QUAD4_A_V1) GCA_000349065.1 net
A. sinensisAnopheles sinensis Jul. 2014 (AS2) GCA_000441895.2 net
A. stephensiAnopheles stephensi Sep. 2018 (ASM344897v1) GCA_003448975.1 net
Aedes_aegyptiAedes aegypti Jun. 2017 (AaegL5.0) GCF_002204515.2 net
Aedes_albopictusAedes albopictus Jan. 2017 (canu_80X_arrow2.2) GCF_001876365.2 net
Bactrocera_dorsalisBactrocera dorsalis Dec. 2014 (ASM78921v2) GCF_000789215.1 net
Bactrocera_latifronsBactrocera latifrons Oct. 2016 (ASM185335v1) GCF_001853355.1 net
Bactrocera_oleaeBactrocera oleae Jul. 2015 (gapfilled_joined_lt9474.gt500.covgt10) GCF_001188975.1 net
Bactrocera_tryoniBactrocera tryoni May 2014 (Assembly_2.2_of_Bactrocera_tryoni_genome) GCA_000695345.1 net
Belgica_antarcticaBelgica antarctica Sep. 2014 (ASM77530v1) GCA_000775305.1 net
Calliphora_vicinaCalliphora vicina Jun. 2015 (ASM101727v1) GCA_001017275.1 net
Ceratitis_capitataCeratitis capitata Nov. 2017 (Ccap_2.1) GCF_000347755.3 net
Chaoborus_trivitattusChaoborus trivitattus May 2015 (ASM101481v1) GCA_001014815.1 net
Chironomus_ripariusChironomus riparius May 2015 (ASM101450v1) GCA_001014505.1 net
Chironomus_tentansChironomus tentans Nov. 2014 (CT01) GCA_000786525.1 net
Cirrula_hiansCirrula hians May 2015 (ASM101507v1) GCA_001015075.1 net
Clogmia_albipunctataClogmia albipunctata May 2015 (ASM101494v1) GCA_001014945.1 net
Clunio_marinusClunio marinus Nov. 2016 (CLUMA_1.0) GCA_900005825.1 net
Coboldia_fuscipesCoboldia fuscipes May 2015 (ASM101433v1) GCA_001014335.1 net
Condylostylus_patibulatusCondylostylus patibulatus May 2015 (ASM101487v1) GCA_001014875.1 net
Culex_quinquefasciatusCulex quinquefasciatus Apr. 2007 (CulPip1.0) GCF_000209185.1 net
Culicoides_sonorensisCulicoides sonorensis Feb. 2018 (Cson_Genome_version_2.0) GCA_900258525.2 net
D. albomicansDrosophila albomicans 21 May 2012 (DroAlb_1.0/droAlb1) 21 May 2012 (DroAlb_1.0/droAlb1) net
D. americanaDrosophila americana Oct. 2015 (D._americana_H5_strain_genome_assembly) GCA_001245395.1 net
D. ananassaeDrosophila ananassae Feb. 2006 (Agencourt CAF1/droAna3) Feb. 2006 (Agencourt CAF1/droAna3) syntenic
D. arizonaeDrosophila arizonae May 2016 (ASM165402v1) GCF_001654025.1 syntenic
D. athabascaDrosophila athabasca Jun. 2018 (ASM318502v1) GCA_003185025.1 syntenic
D. biarmipesDrosophila biarmipes 04 Mar 2013 (Dbia_2.0/droBia2) 04 Mar 2013 (Dbia_2.0/droBia2) syntenic
D. bipectinataDrosophila bipectinata 04 Mar 2013 (Dbip_2.0/droBip2) 04 Mar 2013 (Dbip_2.0/droBip2) net
D. busckiiDrosophila busckii Sep. 2015 (ASM127793v1) GCF_001277935.1 syntenic
D. elegansDrosophila elegans 04 Mar 2013 (Dele_2.0/droEle2) 04 Mar 2013 (Dele_2.0/droEle2) net
D. erectaDrosophila erecta Feb. 2006 (Agencourt CAF1/droEre2) Feb. 2006 (Agencourt CAF1/droEre2) syntenic
D. eugracilisDrosophila eugracilis 04 Mar 2013 (Deug_2.0/droEug2) 04 Mar 2013 (Deug_2.0/droEug2) net
D. ficusphilaDrosophila ficusphila 04 Mar 2013 (Dfic_2.0/droFic2) 04 Mar 2013 (Dfic_2.0/droFic2) net
D. grimshawiDrosophila grimshawi Feb. 2006 (Agencourt CAF1/droGri2) Feb. 2006 (Agencourt CAF1/droGri2) syntenic
D. hydeiDrosophila hydei Nov. 2017 (ASM278046v1) GCF_002780465.1 net
D. kikkawaiDrosophila kikkawai 04 Mar 2013 (Dkik_2.0/droKik2) 04 Mar 2013 (Dkik_2.0/droKik2) net
D. mirandaDrosophila miranda 19 Apr 2013 (DroMir_2.2/droMir2) 19 Apr 2013 (DroMir_2.2/droMir2) syntenic
D. mojavensisDrosophila mojavensis Feb. 2006 (Agencourt CAF1/droMoj3) Feb. 2006 (Agencourt CAF1/droMoj3) syntenic
D. montanaDrosophila montana May 2018 (ASM308661v1) GCA_003086615.1 net
D. nasutaDrosophila nasuta Jul. 2017 (ASM222288v1) GCA_002222885.1 net
D. navojoaDrosophila navojoa May 2016 (ASM165401v1) GCF_001654015.1 syntenic
D. novamexicanaDrosophila novamexicana Jul. 2018 (DnovRS1) GCA_003285875.1 syntenic
D. obscuraDrosophila obscura Jul. 2017 (Dobs_1.0) GCF_002217835.1 net
D. persimilisDrosophila persimilis Oct. 2005 (Broad/droPer1) Oct. 2005 (Broad/droPer1) net
D. pseudoobscuraDrosophila pseudoobscura pseudoobscura 11 Apr 2013 (Dpse_3.0/droPse3) 11 Apr 2013 (Dpse_3.0/droPse3) syntenic
D. pseudoobscura_1Drosophila pseudoobscura pseudoobscura Apr. 2013 (Dpse_3.0) GCF_000001765.3 net
D. rhopaloaDrosophila rhopaloa 22 Feb 2013 (Drho_2.0/droRho2) 22 Feb 2013 (Drho_2.0/droRho2) net
D. sechelliaDrosophila sechellia Oct. 2005 (Broad/droSec1) Oct. 2005 (Broad/droSec1) syntenic
D. serrataDrosophila serrata Apr. 2017 (Dser1.0) GCF_002093755.1 net
D. simulansDrosophila simulans Sep. 2014 (ASM75419v2/droSim2) Sep. 2014 (ASM75419v2/droSim2) syntenic
D. subobscuraDrosophila subobscura Nov. 2017 (Dsub_1.0) GCA_002749795.1 net
D. suzukiiDrosophila suzukii 30 Sep 2013 (Dsuzukii.v01/droSuz1) 30 Sep 2013 (Dsuzukii.v01/droSuz1) net
D. takahashiiDrosophila takahashii 04 Mar 2013 (Dtak_2.0/droTak2) 04 Mar 2013 (Dtak_2.0/droTak2) net
D. virilisDrosophila virilis Feb. 2006 (Agencourt CAF1/droVir3) Feb. 2006 (Agencourt CAF1/droVir3) syntenic
D. willistoniDrosophila willistoni 03 Aug 2006 (dwil_caf1/droWil2) 03 Aug 2006 (dwil_caf1/droWil2) syntenic
D. yakubaDrosophila yakuba 27 Jun 2006 (dyak_caf1/droYak3) 27 Jun 2006 (dyak_caf1/droYak3) syntenic
Ephydra_gracilisEphydra gracilis May 2015 (ASM101467v1) GCA_001014675.1 net
Eristalis_dimidiataEristalis dimidiata May 2015 (ASM101514v1) GCA_001015145.1 net
Eutreta_dianaEutreta diana May 2015 (ASM101511v1) GCA_001015115.1 net
Glossina_austeniGlossina austeni May 2014 (Glossina_austeni-1.0.3) GCA_000688735.1 net
Glossina_brevipalpisGlossina brevipalpis May 2014 (Glossina_brevipalpis_1.0.3) GCA_000671755.1 net
Glossina_fuscipesGlossina fuscipes fuscipes May 2014 (Glossina_fuscipes-3.0.2) GCA_000671735.1 net
Glossina_morsitans_1Glossina morsitans May 2015 (ASM101451v1) GCA_001014515.1 net
Glossina_morsitans_2Glossina morsitans morsitans Mar. 2014 (ASM107743v1) GCA_001077435.1 net
Glossina_pallidipesGlossina pallidipes May 2014 (Glossina_pallidipes-1.0.3) GCA_000688715.1 net
Glossina_palpalis_gambiensisGlossina palpalis gambiensis Jan. 2015 (Glossina_palpalis_gambiensis-2.0.1) GCA_000818775.1 net
Haematobia_irritansHaematobia irritans May 2018 (Hi_v1.0) GCA_003123925.1 net
Hermetia_illucensHermetia illucens May 2015 (ASM101489v1) GCA_001014895.1 net
Holcocephala_fuscaHolcocephala fusca May 2015 (ASM101521v1) GCA_001015215.1 net
Liriomyza_trifoliiLiriomyza trifolii May 2015 (ASM101493v1) GCA_001014935.1 net
Lucilia_cuprinaLucilia cuprina Dec. 2017 (Lcup_2.0) GCF_000699065.1 net
Lucilia_sericataLucilia sericata May 2015 (ASM101483v1) GCA_001014835.1 net
Lutzomyia_longipalpisLutzomyia longipalpis Jun. 2012 (Llon_1.0) GCA_000265325.1 net
M. domesticaMusca domestica 22 Apr 2013 (Musca_domestica-2.0.2/musDom2) 22 Apr 2013 (Musca_domestica-2.0.2/musDom2) net
Mayetiola_destructorMayetiola destructor Oct. 2010 (Mdes_1.0) GCA_000149185.1 net
Megaselia_abditaMegaselia abdita May 2015 (ASM101517v1) GCA_001015175.1 net
Megaselia_scalarisMegaselia scalaris Mar. 2013 (ASM34191v2) GCA_000341915.2 net
Mochlonyx_cinctipesMochlonyx cinctipes May 2015 (ASM101484v1) GCA_001014845.1 net
Neobellieria_bullataNeobellieria bullata Jun. 2015 (ASM101745v1) GCA_001017455.1 net
Paykullia_maculataPaykullia maculata Apr. 2018 (ASM305512v1) GCA_003055125.1 net
Phlebotomus_papatasiPhlebotomus papatasi May 2012 (Ppap_1.0) GCA_000262795.1 net
Phormia_reginaPhormia regina Sep. 2016 (ASM173554v1) GCA_001735545.1 net
Phortica_variegataPhortica variegata May 2015 (ASM101441v1) GCA_001014415.1 net
Proctacanthus_coquillettiProctacanthus coquilletti Jan. 2017 (200kmer_750.trimmed) GCA_001932985.1 net
Rhagoletis_zephyriaRhagoletis zephyria Jul. 2016 (Rhagoletis_zephyria_1.0) GCF_001687245.1 net
Sarcophagidae_BV_2014Sarcophagidae sp. BV-2014 Jul. 2015 (ASM104719v1) GCA_001047195.1 net
Scaptodrosophila_lebanonensisScaptodrosophila lebanonensis Jul. 2018 (SlebRS1) GCA_003285725.1 net
Sphyracephala_brevicornisSphyracephala brevicornis May 2015 (ASM101523v1) GCA_001015235.1 net
Stomoxys_calcitransStomoxys calcitrans May 2015 (Stomoxys_calcitrans-1.0.1) GCF_001015335.1 net
T. castaneumTribolium castaneum Sep. 2005 (Baylor 2.0/triCas2) Sep. 2005 (Baylor 2.0/triCas2) net
Teleopsis_dalmanniTeleopsis dalmanni Jul. 2017 (Tel_dalmanni_2A_v1.0) GCA_002237135.1 net
Tephritis_californicaTephritis californica Jun. 2015 (ASM101751v1) GCA_001017515.1 net
Themira_minorThemira minor May 2015 (ASM101457v1) GCA_001014575.1 net
Tipula_oleraceaTipula oleracea Jun. 2015 (ASM101753v1) GCA_001017535.1 net
Trichoceridae_BV_2014Trichoceridae sp. BV-2014 May 2015 (ASM101442v1) GCA_001014425.1 net
Trupanea_jonesiTrupanea jonesi May 2015 (ASM101466v1) GCA_001014665.1 net
Zaprionus_indianusZaprionus indianus Oct. 2016 (ZP_IN_1.0) GCA_001752445.1 net
Zeugodacus_cucurbitaeZeugodacus cucurbitae Dec. 2014 (ASM80634v1) GCF_000806345.1 net

Downloads for data in this track are available:

Display Conventions and Configuration

The track configuration options allow the user to display the three different clade sets of scores, all, Brachycera, Nematocera or Holometabola, 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 D. melanogaster 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 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 D. melanogaster 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 D. melanogaster 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 D. melanogaster sequence at those alignment positions relative to the longest non-D. melanogaster 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 GenesD. persimilis
Ensembl Genes v68D. erecta, D. ananassae, D. melanogaster
Xeno RefGeneD. sechellia
no annotationsall others
Table 2. Gene tracks used for codon translation.


Pairwise alignments with the D. melanogaster 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 parameters for 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 124-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 some were filtered to retain only alignments of best quality in both the target and query ("reciprocal best"). See also: D. melanogaster/dm6 124-way alignment filtering parameters. The column alignment type indicates the type of filtering.

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 124-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.


Phylip distance operations:

Fan H, Ives A, Surget_groba Y, Cannon C. An assembly and alignment-free method of phylogeny reconstruction from next-generation sequencing data. BMC Genomics. 2015; 16(1): 522. PMID: 26169061

Bernard G, Ragan M, Chana C.X. Recapitulating phylogenies using k-mers: from trees to networks. F1000Res. 2016; 5: 2789. PMID: 28105314

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