Galaxy provides tools for extracting subsets of genomic sequences and alignments. Currently the public instance of Galaxy supports the following sequences and alignments
28 sequences are available in Galaxy (not including Main/DataLibraries/Microbes):
| Build | Species | Clade |
| anoGam1 | A. gambiae | Insect |
| bosTau2 | Cow | Vertebrate |
| canFam1 | Dog | Vertebrate |
| canFam2 | Dog | Vertebrate |
| ce2 | C. elegans | Nematode |
| danRer2 | Zebrafish | Vertebrate |
| danRer3 | Zebrafish | Vertebrate |
| danRer4 | Zebrafish | Vertebrate |
| dm2 | D. melanogaster | Insect |
| dp3 | D. pseudoobscura | Insect |
| droSim1 | D. simulans | Insect |
| droYak2 | D. yakuba | Insect |
| fr1 | Fugu | Vertebrate |
| galGal2 | Chicken | Vertebrate |
| hg16 | Human | Vertebrate |
| hg17 | Human | Vertebrate |
| hg18 | Human | Vertebrate |
| musMus6 | Mouse | Vertebrate |
| musMus7 | Mouse | Vertebrate |
| musMus8 | Mouse | Vertebrate |
| monDom4 | Opossum | Vertebrate |
| panTro1 | Chimpanzee | Vertebrate |
| panTro2 | Chimpanzee | Vertebrate |
| rheMac2 | Rhesus | Vertebrate |
| ratNor3 | Rat | Vertebrate |
| ratNor4 | Rat | Vertebrate |
| sacCer1 | Yeast (S. cerevisiae) | Other |
| tetNig1 | Tetraodon | Vertebrate |
156 pairwise alignments are available in Galaxy:
| Build | Aligned with |
| anoGam1 | dm1 |
| dm2 | |
| canFam1 | hg17 |
| musMus6 | |
| canFam2 | canFam2 |
| hg17 | |
| hg18 | |
| musMus6 | |
| musMus7 | |
| musMus8 | |
| ratNor3 | |
| ratNor4 | |
| danRer2 | fr1 |
| hg17 | |
| musMus6 | |
| tetNig1 | |
| danRer3 | fr1 |
| hg18 | |
| musMus7 | |
| musMus8 | |
| tetNig1 | |
| danRer4 | fr1 |
| hg18 | |
| musMus8 | |
| ratNor4 | |
| tetNig1 | |
| dm2 | anoGam1 |
| apiMel1 | |
| apiMel2 | |
| dp2 | |
| dp3 | |
| droAna1 | |
| droMoj1 | |
| droPer1 | |
| droSec1 | |
| droSim1 | |
| droVir1 | |
| droYak1 | |
| dp3 | dm2 |
| droSim1 | dm2 |
| droYak2 | dm2 |
| fr1 | danRer2 |
| danRer3 | |
| danRer4 | |
| hg18 | |
| musMus6 | |
| musMus7 | |
| musMus8 | |
| galGal2 | danRer2 |
| hg16 | |
| hg17 | |
| hg18 | |
| musMus6 | |
| musMus7 | |
| musMus8 | |
| monDom1 | |
| ratNor4 | |
| tetNig1 | |
| xenTro1 | |
| hg16 | musMus3 |
| mm4 | |
| musMus6 | |
| panTro1 | |
| ratNor3 | |
| hg17 | bosTau1 |
| bosTau2 | |
| canFam1 | |
| canFam2 | |
| danRer1 | |
| danRer2 | |
| danRer3 | |
| fr1 | |
| galGal2 | |
| musMus5 | |
| musMus6 | |
| musMus7 | |
| monDom1 | |
| panTro1 | |
| rheMac1 | |
| rheMac2 | |
| ratNor3 | |
| tetNig1 | |
| hg18 | bosTau2 |
| canFam2 | |
| danRer3 | |
| danRer4 | |
| fr1 | |
| galGal2 | |
| musMus7 | |
| musMus8 | |
| panTro1 | |
| rheMac2 | |
| ratNor4 | |
| tetNig1 | |
| xenTro1 | |
| musMus6 | bosTau1 |
| canFam1 | |
| danRer2 | |
| fr1 | |
| galGal2 | |
| hg16 | |
| hg17 | |
| monDom1 | |
| panTro1 | |
| ratNor3 | |
| tetNig1 | |
| xenTro1 | |
| musMus7 | bosTau2 |
| canFam2 | |
| danRer3 | |
| fr1 | |
| galGal2 | |
| hg17 | |
| hg18 | |
| panTro1 | |
| rheMac1 | |
| ratNor3 | |
| tetNig1 | |
| xenTro1 | |
| musMus8 | bosTau2 |
| canFam2 | |
| danRer3 | |
| danRer4 | |
| fr1 | |
| galGal2 | |
| hg17 | |
| hg18 | |
| monDom4 | |
| panTro1 | |
| rheMac2 | |
| ratNor4 | |
| tetNig1 | |
| xenTro1 | |
| xenTro2 | |
| panTro1 | hg16 |
| hg18 | |
| musMus6 | |
| musMus7 | |
| musMus8 | |
| rheMac2 | hg18 |
| musMus8 | |
| ratNor4 | |
| ratNor3 | hg18 |
| musMus8 | |
| ratNor4 | |
| ratNor4 | hg18 |
| musMus8 | |
| ratNor4 | |
| tetNig1 | danRer3 |
| danRer4 | |
| fr1 | |
| hg17 | |
| hg18 | |
| musMus6 | |
| musMus7 | |
| musMus8 |
4 multiZ alignments are available in Galaxy:
- hg17-panTro1-musMus5-ratNor3-canFam1-galGal2-fugRub1-danRer1
- hg18-panTro1-bosTau2-rheMac2-musMus8-ratNor4-canFam2-echTel1-loxAfr1-oryCun1-danRer3-monDom4-dasNov1-galGal2-fr1-tetNig1-xenTro1
- hg18-panTro2-rheMac2-musMus8-canFam2
- hg18-panTro2-rheMac2