MrBayes2.01
15 August 2001
(c) John Huelsenbeck & Fredrik Ronquist

1. Known problems (version 2.01)

The program will not interpret information after the first MrBayes block
correctly. This will be corrected in version 3. For now, make sure there is only
one MrBayes block in each batch file.

The 'sumt' and 'sump' commands are not able to deal with '.t' and '.p' files that
contain information from several runs. Thus, if you append the results from one
run to those of other runs, you need to delete all the information from the
previous run(s) before running 'sumt' or 'sump' on the '.t' or '.p' file. In
version 3, 'sumt' and 'sump' will summarize the information in the last block in
the '.t' or '.p' file.

The program does not handle execute statements in batch files correctly. The file
that is called is executed correctly but when returning to the calling file the
command parser inappropriately thinks it is outside of any block. This problem can
be solved by inserting 'begin mrbayes;' after the execute statement in the calling
file. This will be corrected in version 3.

After the program executes a 'sumt' or a 'sump' command in a batch file, the
following lines are interpreted incorrectly. Again, this problem can be solved by
inserting 'begin mrbayes;' after the 'sumt' or 'sump' command. This will be
corrected in version 3.


2. Version history
 
Version 2.01
----------------------------------

The #NEXUS file header is now printed correctly to output files.

A problem with the invariant and invariant gamma models in all previous versions
of the program is now corrected. The bug caused long chains to stop with the error
message "WARNING: In LIKE_EPSILON".

Memory leaks introduced in version 2.0 have been deleted. The usual symptom of
these bugs would be termination of a chain after many generations with an error
message such as "ERROR: Problem allocating " and then the name of some variable.

The tokens in the translate command are now printed in the correct order in the
file containing the consensus tree (the .con file).

Several bugs in the likelihood functions for the standard and restriction models
are now fixed. The bugs would crash the program when these models were invoked.

A bug that caused the program to crash when it was asked to open a non-existing
file is now fixed.


Version 2.0
-----------------------------------------

All likelihood functions are completely rewritten, resulting in significant speed
gains for most data types.

Models for restriction sites and for standard binary characters have been added.

Parsimony model (Tuffley & Steel) has been added.

New topology and branch length move types have been introduced.

User can set proposal probabilities of different move types.

The sumt command outputs a consensus tree with posterior clade probabilities in
addition to partition frequencies. If branch lengths are saved, a consensus
phylogram is output as well.


3. Bug reports

Send bug reports to
John Huelsenbeck <johnh@brahms.biology.rochester.edu>
or Fredrik Ronquist <fredrik.ronquist@ebc.uu.se>.

===============================

Plan 9 port by Peter A. Cejchan <pac7@post.cz> Mon Dec 9 06:53:19 EST 2002
Changes in sources (if any) marked '++pac'. Type 'mk install' to compile and
install. Enjoy!