Multiple genome alignments

Multiple alignments are calculated between groups of genomes.

Alignments available

NameGenomesMethod used
wormbase-ws269 cactus-halBrugia malayi (Nematode, FR3), Caenorhabditis brenneri (Nematode), Caenorhabditis briggsae (Nematode), Caenorhabditis elegans (Nematode, N2), Caenorhabditis japonica (Nematode), Caenorhabditis remanei (Nematode), Onchocerca volvulus (Nematode, O. volvulus Cameroon isolate), Pristionchus pacificus (Nematode, PS312), Strongyloides ratti (Threadworm)Cactus
40 pangenome_drosophilaBactrocera neohumeralis (Lesser Queensland fruit fly, Rockhampton), Coremacera marginata (Sieve-winged Snailkiller, reference), Drosophila albomicans (Fruit fly, 15112-1751.03), Drosophila ananassae (Fruit fly, 14024-0371.13), Drosophila arizonae (Fruit fly, ariz_Son04), Drosophila biarmipes (Fruit fly, raj3), Drosophila bipectinata (Fruit fly), Drosophila busckii (Fruit fly, San Diego stock center stock number 13000-0081.31), Drosophila elegans (Fruit fly), Drosophila erecta (Fruit fly, 14021-0224.00,06,07), Drosophila eugracilis (Fruit fly, 14026-0451.02), Drosophila ficusphila (Fruit fly, 14025-0441.05), Drosophila grimshawi (Fruit fly, 15287-2541.00), Drosophila guanche (Fruit fly), Drosophila gunungcola (Fruit fly, Sukarami), Drosophila hydei (Fruit fly, 15085-1641.00,03,60), Drosophila innubila (Fruit fly, TH190305), Drosophila kikkawai (Fruit fly, 14028-0561.14), Drosophila mauritiana (Fruit fly, mau12), Drosophila melanogaster (Fruit fly), Drosophila miranda (Fruit fly, MSH22), Drosophila mojavensis (Fruit fly, 15081-1352.22), Drosophila navojoa (Fruit fly, navoj_Jal97), Drosophila obscura (Fruit fly, BZ-5 IFL), Drosophila persimilis (Fruit fly, 14011-0111.01,24,50), Drosophila pseudoobscura (Fruit fly, MV2-25), Drosophila rhopaloa (Fruit fly, 14029-0021.01), Drosophila santomea (Fruit fly, STO CAGO 1482), Drosophila sechellia (Fruit fly, sech25), Drosophila simulans (Fruit fly, w501), Drosophila subobscura (Fruit fly, 14011-0131.10), Drosophila subpulchrella (Fruit fly, 33 F10 #4), Drosophila suzukii (Fruit fly, WT3_2.0), Drosophila takahashii (Fruit fly, IR98-3 E-12201), Drosophila teissieri (Fruit fly, GT53w), Drosophila virilis (Fruit fly, 15010-1051.48,49,85), Drosophila willistoni (Fruit fly, 14030-0811.24), Drosophila yakuba (Fruit fly, Tai18E2), Machimus atricapillus (Kite-tailed Robberfly, reference), Myopa tessellatipennis (Thick-headed flies, reference)Cactus

Alignment methods

Progressive Cactus

Progressive-Cactus is a next-generation aligner that stores whole-genome alignments in a graph structure. Genomes can be added incrementally, which makes it scalable to hundreds of genomes. Further details on these methods can be found in Algorithms for genome multiple sequence alignment and Cactus graphs for genome comparisons.