comparative genomics tools - whole genome alignments

Here you could find whole genome alignments for different genome pairs, these alignments are usually crucial for a comparative genomic study.

http://pipeline.lbl.gov/downloads.shtml

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