Tools for Comparative Genomics

You will find at this page the whole genome alignments generated by the Berkeley Genome Pipeline, as well as the Pipeline software.

Please note that many of the data listed below, including assemblies used for the alignments, are unpublished - we ask that you respect the scientific contributions of the data producers (see, for example, NHGRI Rapid Data Release Policy).


Human Feb. 2009

Human - Chimp 03-May-2013
Human - Mouse Jul. 2007 24-Jun-2010

Human Mar. 2006

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 (May 2004) - 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 (TAIR10)

Arabidopsis - A. lyrata v.1.0 17-Apr-2009
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

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.3.0

Poplar - Eucalyptus 01-Aug-2012

Poplar v.2.0

Poplar - Rice v.6.0 23-Dec-2009
Poplar - Papaya 26-Dec-2009

Poplar v.1.1

Poplar - Arabidopsis 11-Aug-2005
Poplar - Rice v.3.0 11-Aug-2005
Poplar - Poplar 11-Aug-2005

Rice v.6.0

Rice - Papaya 26-Dec-2009
Rice - Maize B73 v.2 17-Jun-2010

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 BACs 06-Jun-2007
Sorghum - Maize B73 v.2 18-Jun-2010

Eucalyptus v.1.0

Eucalyptus - Eucalyptus 07-Jan-2011

Common bean v.1.0

Common bean - Medicago 26-Jul-2012

B. distachyon v.1.0

B. distachyon - Rice v.6.0 28-Dec-2009
B. distachyon - Sorghum v.1.0 05-Feb-2009
B. distachyon - Maize B73 v.2 17-Jun-2010

Cucumber v.1

Cucumber - Rice v.7.0 30-Nov-2011
Cucumber - Maize B73 v.2 17-Jun-2010
Cucumber - A. thaliana (TAIR10) 24-Dec-2009
Cucumber - Poplar v.3.0 24-Jul-2012
Cucumber - M. truncatula Mt4.0 18-Dec-2013
Cucumber - Sweet orange v.1.0 16-Jul-2010
Cucumber - Sorghum v.1.0 29-Dec-2009
Cucumber - Soybean v.2.0 19-Dec-2013
Cucumber - Wine grape 16-Jul-2010
Cucumber - A. lyrata v.1.0 25-Dec-2009
Cucumber - Papaya 26-Dec-2009
Cucumber - B. distachyon v.1.0 30-Dec-2009
Cucumber - Cassava v.4 13-Jul-2010
Cucumber - Castor bean release 0.1 20-Dec-2009
Cucumber - Cucumber 08-Feb-2010
Cucumber - Monkey flower v.2.0 25-Apr-2013
Cucumber - Peach v.1.0 12-May-2010
Cucumber - Columbine v.1.0 16-Jul-2010
Cucumber - Eucalyptus v.1.0 22-Dec-2010
Cucumber - Common bean v.1.0 25-Jul-2012
Cucumber - Flax v.1.0 19-Dec-2011
Cucumber - Apple v.1.0 24-Dec-2011
Cucumber - Strawberry v.1.1 26-Jul-2012

O. sativa

Nipponbare - 9311 04-Nov-2014
Nipponbare - IR64 19-Jan-2015
Nipponbare - Kasalath 05-Nov-2014
Nipponbare - DJ123 05-Nov-2014
9311 - IR64 19-Jan-2015
9311 - Kasalath 05-Nov-2014
9311 - DJ123 06-Nov-2014
IR64 - Kasalath 19-Jan-2015
IR64 - DJ123 19-Jan-2015
Kasalath - DJ123 07-Nov-2014

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 found here. Contact for help and comments.