You will find at this page the whole genome alignments generated by the Berkeley Genome Pipeline, as well as the Pipeline software.
If the whole genome alignments you wish to download are not listed on this page, please send an email to vista@lbl.gov
.Please note that many of the data listed below, including assemblies used for the alignments, are unpublished - we ask that you respect the scientific contributions of the data producers (see, for example, NHGRI Rapid Data Release Policy).
Alignments
| Human - Rhesus - Horse - Dog - Mouse - Rat - Chicken | 14-May-2008 |
| Human - Orangutan - Rhesus - Marmoset | 14-Dec-2007 |
| Human - Chimp | 09-Apr-2007 |
| Human - Dog | 02-Apr-2007 |
| Human - Mouse | 27-Mar-2007 |
| Human - Dog - Mouse - Rat - Chicken | 3-Dec-2006 |
| Human (Jul. 2003) - Mouse - Rat | 14-Mar-2004 |
| Human (Apr. 2003) - Mouse - Rat | 22-Aug-2003 |
A. thaliana Jun. 2009 (TAIR9)
| Arabidopsis - Maize B73 v.2 | 16-Jun-2010 |
| Arabidopsis - M. esculenta v.4 | 13-Jul-2010 |
| Arabidopsis - M. guttatus v.1.0 | 27-Dec-2009 |
| Arabidopsis - M. truncatula Mt3.0 | 25-Dec-2009 |
| Arabidopsis - Papaya | 25-Dec-2009 |
| Arabidopsis - Poplar v.2.0 | 23-Dec-2009 |
| Arabidopsis - P. patens v.1.1 | 07-Feb-2010 |
| Arabidopsis - Rice v.6.0 | 25-Dec-2009 |
| Arabidopsis - S. moellendorffii v.1.0 | 08-Feb-2010 |
| Arabidopsis - Soybean | 24-Dec-2009 |
| Arabidopsis - Wine grape | 17-Jul-2010 |
| Arabidopsis - A. lyrata - T. halophila - C. papaya - C. clementina | 11-Mar-2011 |
Poplar v.2.0
| Poplar - Rice v.6.0 | 23-Dec-2009 |
| Poplar - Papaya | 26-Dec-2009 |
Rice v.6.0
| Rice - Papaya | 26-Dec-2009 |
A. thaliana Apr. 2008 (TAIR8)
| Arabidopsis - A. lyrata | 30-Jul-2008 |
| Arabidopsis - Soybean | 03-Dec-2008 |
| Arabidopsis - Poplar v.1.1 | 30-Sep-2008 |
| Arabidopsis - Medicago | 18-Dec-2008 |
| Arabidopsis - Papaya | 17-Dec-2008 |
| Arabidopsis - Wine grape | 15-Aug-2008 |
A. thaliana Mar. 2004
| Arabidopsis - Rice v.1.0 | 28-Jan-2005 |
| Arabidopsis - Sorghum | 04-Jan-2008 |
| Arabidopsis - Poplar v.1.1 | 11-Aug-2005 |
Poplar v.1.1
| Poplar - Arabidopsis | 11-Aug-2005 |
| Poplar - Rice v.3.0 | 11-Aug-2005 |
| Poplar - Poplar | 11-Aug-2005 |
Sorghum v.1.0
| Sorghum - Arabidopsis - Rice v.5.0 | 22-Apr-2008 |
| Sorghum - Sorghum | 23-May-2007 |
| Sorghum - Rice v.5.0 | 10-Apr-2007 |
| Sorghum - Rice v.6.0 | 28-Dec-2009 |
| Sorghum - Maize | 06-Jun-2007 |
A. niger v.1.0
| A. niger - A. fumigatus | 23-Mar-2006 |
| A. niger - A. nidulans | 16-Mar-2006 |
| A. niger - A. oryzae | 23-Mar-2006 |
D. melanogaster Oct. 2006
| D. melanogaster - D. pseudoobscura - D. yakuba - D. ananassae - D. erecta - D. simulans | 13-Mar-2008 |
D. melanogaster Apr. 2004
| D. melanogaster - D. simulans | 15-July-2005 |
| D. melanogaster - D. pseudoobscura | 29-Mar-2005 |
| D. melanogaster - D. ananassae | 29-Mar-2005 |
| D. melanogaster - D. mojavensis | 29-Mar-2005 |
| D. melanogaster - D. yakuba | 29-Mar-2005 |
| D. melanogaster - D. virilis | 29-Mar-2005 |
| D. melanogaster - D. erecta | 29-Mar-2005 |
D. melanogaster Jan. 2003
| D. melanogaster - D. pseudoobscura (LAGAN) | 20-Sep-2004 |
| D. melanogaster - D. pseudoobscura (AVID) | 13-Aug-2004 |
| D. melanogaster - D. ananassae | 20-Sep-2004 |
| D. melanogaster - D. mojavensis | 20-Sep-2004 |
| D. melanogaster - D. virilis | 21-Sep-2004 |
| D. melanogaster - D. yakuba | 21-Aug-2004 |
| Ciona intestinalis v.1.0 - Ciona savignyi | 13-Aug-2004 |
| Ciona intestinalis v.2.0 - Ciona savignyi | 29-Nov-2005 |
| Human (NCBI build 30) - Mouse (MGSCv3) (all alignments) | 04-Nov-2002 |
| Human (NCBI build 30) - Mouse (MGSCv3) (filtered alignments) | 4-Nov-2002 |
| Notes for this run | |
| Escherichia coli O6 CFT073 | 25-May-2005 SLAGAN |
Pipeline Software:
The complete source code can be downloaded by clicking the "I agree" button after
reading the End User License Agreement.
Contact vista@lbl.gov
for help and comments.
