update *beast tutorial

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4921 ca793f91-a31e-0410-b540-2769d408b6a1
and xml

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4922 ca793f91-a31e-0410-b540-2769d408b6a1
Issue 609:	BEAUti duplicate prefix issue for multi-partition

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4924 ca793f91-a31e-0410-b540-2769d408b6a1
merge Issue 621 to 1.7

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4927 ca793f91-a31e-0410-b540-2769d408b6a1
Merged fix for local clock issue from trunk.

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4929 ca793f91-a31e-0410-b540-2769d408b6a1
Demoted the non-beagle form of AncestralTreeLikelihood (parser now specifies BEAGLE is required).

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4931 ca793f91-a31e-0410-b540-2769d408b6a1
New experimental farm-farm transmission model

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4933 ca793f91-a31e-0410-b540-2769d408b6a1
Branch 1.7: solve Issue 622:	BEAUti: the "big" updown operator is missing for *BEAST when calibration

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4947 ca793f91-a31e-0410-b540-2769d408b6a1
Removing an in-progress model from the 1.7 branch.

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4965 ca793f91-a31e-0410-b540-2769d408b6a1
Porting fix for issue 611 from trunk. http://code.google.com/p/beast-mcmc/issues/detail?id=611

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4968 ca793f91-a31e-0410-b540-2769d408b6a1
Porting from trunk: Fix for issue 625: http://code.google.com/p/beast-mcmc/issues/detail?id=625
TreeLikelihood for a non codon-partitioned partition was not being given the correct prefix if there was another codon-partitioned partition.


git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4969 ca793f91-a31e-0410-b540-2769d408b6a1
Porting from trunk: http://code.google.com/p/beast-mcmc/issues/detail?id=627

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4974 ca793f91-a31e-0410-b540-2769d408b6a1
Porting from trunk: http://code.google.com/p/beast-mcmc/issues/detail?id=623

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4976 ca793f91-a31e-0410-b540-2769d408b6a1
Porting from trunk: http://code.google.com/p/beast-mcmc/issues/detail?id=620

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4978 ca793f91-a31e-0410-b540-2769d408b6a1
Fix for issue http://code.google.com/p/beast-mcmc/issues/detail?id=629 ported from trunk.

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4980 ca793f91-a31e-0410-b540-2769d408b6a1
Port of commit from trunk.

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4983 ca793f91-a31e-0410-b540-2769d408b6a1
Port of commit from trunk.

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4986 ca793f91-a31e-0410-b540-2769d408b6a1
Branch 1.7: Merge r4950 into 1.7 branch which solved  issue 618

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4988 ca793f91-a31e-0410-b540-2769d408b6a1
Branch 1.7: update read me and version history

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4989 ca793f91-a31e-0410-b540-2769d408b6a1
Branch 1.7: update read me and version history

git-svn-id: http://beast-mcmc.googlecode.com/svn/branches/1.7@4993 ca793f91-a31e-0410-b540-2769d408b6a1