Drosophila Conservation (36 Species) Track Settings
ROAST Alignment and Conservation (36 RefSeq Drosophila Genomes)   (All Comparative Genomics tracks)

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

Species selection:  + -

d. mauritiana
d. sechellia
d. simulans
d. yakuba
d. santomea
d. teissieri
d. erecta
d. ficusphila
d. suzukii
d. subpulchrella
d. biarmipes
d. takahashii
d. eugracilis
d. rhopaloa
d. elegans
d. kikkawai
d. serrata
d. bipectinata
d. ananassae
d. pseudoobscura
d. persimilis
d. miranda
d. guanche
d. subobscura
d. obscura
d. willistoni
d. arizonae
d. mojavensis
d. navojoa
d. hydei
d. virilis
d. novamexicana
d. albomicans
d. grimshawi
d. busckii

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
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 Conserved Elements  Conserved Elements Identified by PhastCons (36 Species)   Schema 
 Basewise Conservation (phastCons)  Basewise Conservation of 36 Drosophila Genomes (phastCons)   Schema 
 Basewise Conservation (phyloP)  Basewise Conservation of 36 Drosophila Genomes (phyloP)   Schema 
 ROAST (36 Species)  ROAST Alignments for 36 Drosophila Species   Schema 


This track shows the multiple genome alignment of 36 Drosophila species. It also shows the measurements of evolutionary conservation using phastCons and phyloP from the Phylogenetic Analysis with Space/Time models (PHAST) package.


Whole Genome Alignments

The genome assemblies for 35 Drosophila species were obtained from the NCBI RefSeq database. Each Drosophila genome assembly was aligned against the Drosophila melanogaster (dm6) assembly using LAST. The following table shows the 36 Drosophila genome assemblies used to construct the ROAST Alignments track:

SpeciesAssembly NameRefSeq AccessionUCSC Assembly
Drosophila melanogasterRelease 6 plus ISO1 MTGCF_000001215.4dm6
Drosophila mauritianaASM438214v1GCF_004382145.1DmauRefSeq1
Drosophila sechelliaASM438219v1GCF_004382195.1DsecRefSeq1
Drosophila simulansPrin_Dsim_3.1GCF_016746395.2DsimRefSeq3
Drosophila yakubaPrin_Dyak_Tai18E2_2.1GCF_016746365.2DyakRefSeq3
Drosophila santomeaPrin_Dsan_1.1GCF_016746245.2DsanRefSeq2
Drosophila teissieriPrin_Dtei_1.1GCF_016746235.2DteiRefSeq1
Drosophila erectaDereRS2GCF_003286155.1DereRefSeq1
Drosophila ficusphilaASM1815226v1GCF_018152265.1DficRefSeq2
Drosophila suzukiiLBDM_Dsuz_2.1.priGCF_013340165.1DsuzRefSeq2
Drosophila subpulchrellaRU_Dsub_v1.1GCF_014743375.2DspuRefSeq1
Drosophila biarmipesASM1814893v1GCF_018148935.1DbiaRefSeq2
Drosophila takahashiiASM1815269v1GCF_018152695.1DtakRefSeq2
Drosophila eugracilisASM1815383v1GCF_018153835.1DeugRefSeq2
Drosophila rhopaloaASM1815211v1GCF_018152115.1DrhoRefSeq2
Drosophila elegansASM1815250v1GCF_018152505.1DeleRefSeq2
Drosophila kikkawaiASM1815253v1GCF_018152535.1DkikRefSeq2
Drosophila serrataDser1.0GCF_002093755.1DserRefSeq1
Drosophila bipectinataASM1815384v1GCF_018153845.1DbipRefSeq2
Drosophila ananassaeASM1763931v2GCF_017639315.1DanaRefSeq2
Drosophila pseudoobscuraUCI_Dpse_MV25GCF_009870125.1DpseRefSeq1
Drosophila persimilisDperRS2GCF_003286085.1DperRefSeq1
Drosophila mirandaD.miranda_PacBio2.1GCF_003369915.1DmirRefSeq1
Drosophila guancheDGUA_6GCF_900245975.1DguaRefSeq1
Drosophila subobscuraUCBerk_Dsub_1.0GCF_008121235.1DsobRefSeq1
Drosophila obscuraASM1815110v1GCF_018151105.1DobsRefSeq2
Drosophila willistoniUCI_dwil_1.1GCF_018902025.1DwilRefSeq2
Drosophila arizonaeASM165402v1GCF_001654025.1DariRefSeq1
Drosophila mojavensisASM1815372v1GCF_018153725.1DmojRefSeq2
Drosophila navojoaUFRJ_Dnav_4.2GCF_001654015.2DnavRefSeq1
Drosophila hydeiDhydRS2GCF_003285905.1DhydRefSeq1
Drosophila virilisDvirRS2GCF_003285735.1DvirRefSeq1
Drosophila novamexicanaDnovRS2.1GCF_003285875.2DnovRefSeq1
Drosophila albomicansdrosAlbom15112-1751.03v1GCF_009650485.1DalbRefSeq1
Drosophila grimshawiASM1815329v1GCF_018153295.1DgriRefSeq2
Drosophila busckiiASM1175060v1GCF_011750605.1DbusRefSeq1
Phylogenetic tree of 36 Drosophila species

The initial set of whole genome alignments were filtered using the 2-split, post-masked strategy with last-split and last-postmask to construct the one-to-one alignments between D. melanogaster and the target genome. The alignments were then processed using the utilities developed by the UCSC Genome Bioinformatics Group. These whole genome alignments were combined into a multiple sequence alignment using ROAST.

The codon translations associated with the multiple sequence alignment were based on FlyBase release 6.46 for D. melanogaster.

Phylogenetic Tree Model

The non-conserved model used by phastCons and phyloP was constructed by the phyloFit program from the PHAST package based on four-fold degenerate (4d) sites. The 4d sites were defined by the FlyBase gene annotations, and extracted from the multiple sequence alignment using msa_view. The non-conserved phylogenetic model was estimated by phyloFit using the general reversible (REV) substitution model, the EM algorithm, and medium (MED) precision.

PhastCons Conservation

Conserved elements were identified by phastCons using a target coverage of 0.3 and an expected length of 45. The conserved model is defined as a scaled version of the non-conserved model with the scaling factor rho of 0.3.

PhyloP Conservation

The conservation score for each site of the alignment was determined by phyloP using the likelihood ratio test (LRT) and the CONACC mode. Sites with positive scores indicate conservation while sites with negative scores indicate acceleration.

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 value of the score. The conservation wiggles can be configured in a variety of ways to highlight different aspects of the displayed information. (See the "Configuring graph-based tracks" page for details.)

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. The "+" and "-" buttons allow you to select or unselect multiple species at once. 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 following display conventions are used to depict the different types of gaps in the alignment:

  • 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.


Frith MC, Kawaguchi R. Split-alignment of genomes finds orthologies more accurately. Genome Biol. 2015 May 21;16(1):106. doi: 10.1186/s13059-015-0670-9.

Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 2011 Jan;12(1):41-51. doi: 10.1093/bib/bbq072.

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. doi: 10.1073/pnas.1932072100.