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Please note that many of the data listed below, including assemblies used for the alignments, are unpublished - we ask that you respect the scientific contributions of the data producers (see, for example, NHGRI Rapid Data Release Policy).

Alignments

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 vista@lbl.gov for help and comments.