The changes to the non-beta versions are detailed below. If you have encountered any of those problems before, they should be fixed now. If you find further bugs, a report (with complete instructions to reproduce the bug, and preferably a data set) is appreciated. Thanks to all the people who found and reported bugs (indicated in square brackets) .

Fixes/changes to version of February 2004 (March 2004):

Fixes/changes to version of March, 2004 (early April 2004):

Fixes/changes to version of early April, 2004 (May 2004):

Fixes/changes to version of May 2004 (June 2004):

Fixes/changes to version of June, 2004 (July 2004):

Fixes/Changes to version of July, 2004 (August 2004):

Fixes/changes to version of August, 2004 (September 2004):

Fixes/changes to version of September, 2004 (November 2004):

Fixes/changes to version of November, 2004 (December 2004):

Fixes/changes to version of December, 2004 (January 2005):

Fixes/changes to version of January, 2005 (February 2005):

Fixes/changes to the version of February, 2005 (March 2005):

Fixes/changes to the version of March, 2005 (May 2005):

tgroup =0 (groupname) { group_one group_two group_three } ;

or, if groups one, two and three are the only ones which starts with "group_":

tgroup =0 (groupname) { group_ } ;

Fixes/changes to the version of May, 2005 (July 2005):

ptnt begin jobname = @@filename labelname ; return ;

if a "target" file had been defined (with goto=), then the filename can be skipped:

goto= filename; ptnt begin jobname = @@ labelname ; return ;

The end of the text to copy must be indicated with a double @. Aside for instructions to slave task(s), this can simplify the syntax for loops, etc.

Fixes/changes to the version of July, 2005 (September 2005):

Fixes/changes to the version of September 2005 (November 2005):

Fixes changes to the version of November 2005 (December 2005):

Fixes/Changes to the version of December 2005 (February 2006)

Fixes/Changes to the version of February 2006 (March 2006):

Fixes/changes to the version of March, 2006 (April 2006):

Fixes/changes to the version of April, 2006 (May 2006):

Fixes changes to the version of May, 2006 (June 2006):

Fixes/changes to the version of June, 2006 (August 2006):

Fixes/changes to the version of July, 2006:

Fixes/changes to the version of August, 2006 (October 2006; this is now version 1.1):

Fixes/changes to the version of October, 2006 (December 2006):

Fixes/changes to the version of December, 2006 (January 2007):

Fixes/changes to the version of January, 2007 (March 2007):

Fixes/changes to the version of March, 2007 (April 2007):

Fixes/changes to the version of April, 2007 (May 2007):

Fixes/changes to the version of May, 2007 (June 2007):

Fixes/changes to the version of June, 2007 (July 2007):

Fixes/changes to the version of July, 2007 (December 2007):

Fixes/changes to the version of December, 2007 (February 2008):

Fixes/changes to the version of February, 2008 (April 2008):

Homo_sapiens_Vertebrata_

Pan_trgolodites_Vertebrata_

Canis_familiaris_Vertebrata_

Musca_domestica_Arthropoda_

Araneus_diadematus_Arthropoda_

you can then create a taxon group with either of these two groups by typing:

agroup =0 (Vertebrates) :_Vertebrata_ ;

agroup =1 (Arthropods) :_Arthropoda_ ;

You can apply the same logic to taxon names when reading trees in parenthetical notation. Thus,

tread ( ( :_Vertebrata_ ) ( :_Arthropoda ) ) ;

will create a tree in which vertebrates and arthropods are monophyletic groups.

Fixes/changes to the version of April, 2008 (August 2008):

"... increase slack in X and try again..."

but it confusingly said:

"... increase slack to X and try again..."

The value reported is now the value to which the slack should be set.

Fixes/changes to the version of June, 2008 (August 2008):

Fixes/changes to the version of August, 2008 (November 2008):

Fixes/changes to the version of November, 2008 (February 2009):

Fixes/changes to the version of February 2009 (March 2009):

Fixes/changes to the version of March 2009 (April, 2009):

Fixes/changes to the version of May 2009 (June, 2009)

Fixes/changes to the version of June 2009 (July, 2009)

Fixes/changes to the version of July 2009 (September, 2009):

Fixes/changes to the version of September 2009 (October, 2009)

Fixes/changes to the version of October 2009 (December 2009)

Fixes/changes to the version of December 2009 (January 2010)

Fixes/changes to the version of January 2010 (March, 2010)

Fixes/changes to the version of March, 2010 (June, 2010):

Fixes/changes to the version of June-August, 2010 (October, 2010):

Fixes/changes to the version of October, 2010 (April, 2011):

Fixes/changes to the version of April, 2011 (July, 2011):

Fixes/changes to the version of July, 2011 (August, 2011):

Fixes/changes to the version of August, 2011 (September, 2011):

loop 0-1 10

loop 10+1 0

will never get executed, only:

loop 0+1 10

loop 10-1 0

will.

Fixes/changes to the version of September, 2011 (December, 2011):

taxname : :Barychelidae :Theraphosidae :Paratropididae =Theraphosoidina = Mygalomorphae ;

taxname : :Theraphosoidina =Mygalomorphae >Theraphosoidina ;

Fixes/changes to the version of December, 2011 (February, 2012):

Fixes/changes to the version of February, 2012 (March, 2012):

Fixes/changes to the version of March, 2012 (May, 2012):

Fixes/changes to the version of May, 2012 (Sept., 2012):

Fixes/changes to the version of Sept. 2012 (Nov. 2012)

Fixes/changes to the version of Nov. 2012 (Jan. 2013)

Fixes/changes to the version of Jan. 2013 (May 2013):

ttag=; resample; taxname=; export – nexusfile.tre ;

Fixes/changes to the version of May 2013 (Sept 2013):

Fixes/changes to the version of Sept. 2013 (Nov. 2013):

Fixes/changes to the version of Nov. 2013 (Feb. 2014):

Fixes/changes to the version of Feb. 2014 (April 21, 2014):

Fixes/changes to the version of April 2014 (May, 2014):

Fixes/changes to the version of May, 2014 (October, 2014):

Fixes/changes to the version of October, 2014 (December, 2014):

Fixes/changes to the version of December, 2014 (February, 2015):

Fixes/changes to the version of February, 2015 (March, 2015):

Fixes/changes to the version of March, 2015 (June, 2015):

Fixes/changes to the version of June, 2015 (November, 2015) – This is a beta for version 1.5. For this version, Santiago Catalano provided code for calculation of four–point Steiner trees (about 5% of the new code incorporated into the program, used for the initial evaluation of rearrangements during branch swapping); all the rest, as usual, by Yours Truly.

Fixes/changes to the version of Nov. 2015 (Feb. 2016):

Fixes/changes to the version of Feb. 2016 (August 2016).

Fixes/changes to the version of August 2016 (November 2016):

Fixes/changes to the version of November 2016 (March 2017):

Fixes/changes to the version of March 2017 (April 2017, Hong Kong version):

Fixes/changes to the version of April 2017, Hong Kong version (June 2017):