TNT - Recent changes [en]

How do I perform a constrain search?

Xuxim — Thu, 09 Sep 2010 01:22:49 GMT

←Older revision		Revision as of 01:22, 9 September 2010
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	[[Commands/force\|force]] = ( 1 4 5 6 ) ;		[[Commands/force\|force]] = ( 1 4 5 6 ) ;

-	Alternatively of you want to be non-monophyletic:	+	Alternatively if you want it to be non-monophyletic:

	[[Commands/force\|force]] - [ 1 4 5 6 ] ;		[[Commands/force\|force]] - [ 1 4 5 6 ] ;

How to manage several datasets

Sacatalano — Wed, 08 Sep 2010 18:40:50 GMT

←Older revision		Revision as of 18:40, 8 September 2010
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	== Putting each dataset on a different block ==		== Putting each dataset on a different block ==
-	The ~~easist~~ way to work with ~~serveral~~ partitions is to put each partition on a different block. ~~See [[Scopes~~,~~_Sets,_Ranges,_Blocks\|~~Here]] ~~for instructions.~~	+	The easiest way to work with several partitions is to put each partition on a different block. The different blocks may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the block).
		+
		+	Here is an example of a datafile with three partitions:
		+
		+	xread 10 6
		+	&[dna]
		+	One AAT
		+	Two AAC
		+	Three ATT
		+	Four ACC
		+	&[dna]
		+	One AATC
		+	Three CATT
		+	Four CACC
		+	Five CACC
		+	Six CTTT
		+	&[num]
		+	One 011
		+	Two 011
		+	Three 022
		+	Four 022
		+	;
		+	proc/ ;

	== Merging datasets ==		== Merging datasets ==
Line 39:		Line 61:
	Be careful when you remove a file from the list to still have “ @@ “ at the end of all the files except the last and “ ; ” in the last file.		Be careful when you remove a file from the list to still have “ @@ “ at the end of all the files except the last and “ ; ” in the last file.

-	3-. To read the data open the file with the list of the datafiles (file_list.tnt in this case). All the files should be in the same directory. Each dataset will be automatically included on a different block.	+	3-. To read the data open the file with the list of the datafiles (file_list.tnt in this case).
		+	All the files should be in the same directory. Each dataset will be automatically included on a different block. The different files may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the block).

Manual/Data Input

Sacatalano — Wed, 08 Sep 2010 18:25:54 GMT

←Older revision		Revision as of 18:25, 8 September 2010
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	==== [[Continuous characters]] ====		==== [[Continuous characters]] ====
	==== [[Landmark_optimization\|Landmark data]]====		==== [[Landmark_optimization\|Landmark data]]====
-	==== [[How to manage several datasets]]====	+	==== [[How to manage several datasets]]====
-		+
-		+
-		+
-		+
-	~~The different blocks may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the block).~~	+

How to manage several datasets

Sacatalano — Wed, 08 Sep 2010 18:24:51 GMT

←Older revision		Revision as of 18:24, 8 September 2010
(4 intermediate revisions not shown.)
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		+	== Putting each dataset on a different block ==
		+	The easist way to work with serveral partitions is to put each partition on a different block. See [[Scopes,_Sets,_Ranges,_Blocks\|Here]] for instructions.
		+
		+	== Merging datasets ==
	The [[dmerge]] command merges data files, and saves them as blocks; the character names and settings are also merged (in Windows version, File/MergeDataFiles, using Ctrl+Left Mouse Button to select multiple files). The [[dmerge]] command also merges (by using * as argument) the characters with identical character names (in Windows version, with Data/MergeHomonymousCharacters). Some basic rules of correspondence between states and state names must be satisfied.		The [[dmerge]] command merges data files, and saves them as blocks; the character names and settings are also merged (in Windows version, File/MergeDataFiles, using Ctrl+Left Mouse Button to select multiple files). The [[dmerge]] command also merges (by using * as argument) the characters with identical character names (in Windows version, with Data/MergeHomonymousCharacters). Some basic rules of correspondence between states and state names must be satisfied.

	The different blocks may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the block).		The different blocks may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the block).
		+
		+
		+
		+	== Reading several dataset from different files ==
		+	When working with several data partitions, it is sometimes useful to put each partition on a different file (instead of including each partition on a different block within a single file) and build the complete matrix at the moment of reading the data.
		+	Doing that is very simple:
		+
		+	1-. Make a file with the list of all the files to be read (called file_list.tnt for instance). The structure is as follow:
		+
		+	macro=;
		+	xread
		+	30000 700
		+	& [ dna ] @@ 16s.tnt data ;
		+	& [ dna ] @@ 18s.tnt data ;
		+	& [ dna ] @@ 26s.tnt data ;
		+	& [ dna ] @@ matK.tnt data ;
		+	& [ num ] @@ morphology data ;
		+	proc/;
		+
		+	30000 and 700 are the number of characters and taxa respectively but SUMMING over all the datasets. If you do not know the exact number put exaggerated high numbers. When TNT reads the data it informs the real number. subsequently use these numbers'
		+
		+	2-. Include each data partition on a different datafile. The data on each file should be in TNT format with the only difference that the string “label Data” should be in the header of the file. In addition, for all the files except the last, the tail of the file should be “ @@ “
		+	e.g.
		+	Label data
		+	ONE AATGGCTTG
		+	TWO AATGGCTTG
		+	THREE AATGGCTTG
		+	FOUR AATGGCTTG
		+	@@
		+
		+	The last dataset in the list (in our case morphology.tnt) should end with “ ; “ and not with “ @@ “ .
		+	Be careful when you remove a file from the list to still have “ @@ “ at the end of all the files except the last and “ ; ” in the last file.
		+
		+	3-. To read the data open the file with the list of the datafiles (file_list.tnt in this case). All the files should be in the same directory. Each dataset will be automatically included on a different block.

Manual/Character Handling

Sacatalano — Wed, 08 Sep 2010 14:12:27 GMT

←Older revision		Revision as of 14:12, 8 September 2010
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	=====[[Setting transformation costs]]=====		=====[[Setting transformation costs]]=====
	=====[[Optimization-Sinapomorphies]]=====		=====[[Optimization-Sinapomorphies]]=====
-	=====[[Landmark Optimization]]=====	+	=====[[Landmark_optimization\|Landmark Optimization]]=====
	----		----
	'''Path:''' Data/Character Settings		'''Path:''' Data/Character Settings

	[[Image:characters.jpg]]		[[Image:characters.jpg]]

Landmark optimization

Sacatalano — Wed, 08 Sep 2010 14:08:40 GMT

←Older revision		Revision as of 14:08, 8 September 2010
(One intermediate revision not shown.)
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	[[Scripting_Commands/lmwt\|'''lmwt''']]		[[Scripting_Commands/lmwt\|'''lmwt''']]
		+
		+	'''Path:''' Data/Character Settings
		+
		+	[[Image:Lands_setting.jpg]]

Landmark Optimization

Sacatalano — Wed, 08 Sep 2010 14:05:14 GMT

New page

[[Image:Lands_setting.jpg]]

Image:Lands setting.jpg

Sacatalano — Wed, 08 Sep 2010 14:04:04 GMT

uploaded "[[Image:Lands setting.jpg]]"

New page

Manual/Character Handling

Sacatalano — Wed, 08 Sep 2010 14:02:58 GMT

←Older revision		Revision as of 14:02, 8 September 2010
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	=====[[Setting transformation costs]]=====		=====[[Setting transformation costs]]=====
	=====[[Optimization-Sinapomorphies]]=====		=====[[Optimization-Sinapomorphies]]=====
-		+	=====[[Landmark Optimization]]=====
	----		----
	'''Path:''' Data/Character Settings		'''Path:''' Data/Character Settings

	[[Image:characters.jpg]]		[[Image:characters.jpg]]

Manual/Scopes, Sets, Ranges, Blocks

Sacatalano — Wed, 08 Sep 2010 13:39:14 GMT

How to manage several datasets

Sacatalano — Wed, 08 Sep 2010 13:37:52 GMT

←Older revision		Revision as of 13:37, 8 September 2010
Line 1:		Line 1:
	The [[dmerge]] command merges data files, and saves them as blocks; the character names and settings are also merged (in Windows version, File/MergeDataFiles, using Ctrl+Left Mouse Button to select multiple files). The [[dmerge]] command also merges (by using * as argument) the characters with identical character names (in Windows version, with Data/MergeHomonymousCharacters). Some basic rules of correspondence between states and state names must be satisfied.		The [[dmerge]] command merges data files, and saves them as blocks; the character names and settings are also merged (in Windows version, File/MergeDataFiles, using Ctrl+Left Mouse Button to select multiple files). The [[dmerge]] command also merges (by using * as argument) the characters with identical character names (in Windows version, with Data/MergeHomonymousCharacters). Some basic rules of correspondence between states and state names must be satisfied.
		+
		+	The different blocks may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the block).

Alternative formats (Nexus,Fasta)

Sacatalano — Wed, 08 Sep 2010 13:36:17 GMT

←Older revision		Revision as of 13:36, 8 September 2010
Line 2:		Line 2:

	The only Nexus blocks that will be read by TNT are those corresponding to data, trees, and assumptions (commands ctype, usertype, include, exclude, and weights). The data can be read in the "dna," "protein" or "standard" formats only (e.g. format datatype = standard;). Unrecognized commands or blocks are simply ignored or skipped. Note that within the NEXUS file, numbering for taxa or characters starts from 1 (one), not from 0 (zero). You can include TNT commands in the nexus file, at the end of the file, preceded by "begin tnt;" (with an end at the end, which is ignored by TNT; otherwise, PAUP* complains that end of file was found when reading a TNT block).		The only Nexus blocks that will be read by TNT are those corresponding to data, trees, and assumptions (commands ctype, usertype, include, exclude, and weights). The data can be read in the "dna," "protein" or "standard" formats only (e.g. format datatype = standard;). Unrecognized commands or blocks are simply ignored or skipped. Note that within the NEXUS file, numbering for taxa or characters starts from 1 (one), not from 0 (zero). You can include TNT commands in the nexus file, at the end of the file, preceded by "begin tnt;" (with an end at the end, which is ignored by TNT; otherwise, PAUP* complains that end of file was found when reading a TNT block).
		+
		+	TNT also recognizes [[Fasta format]].

Basic format

Sacatalano — Wed, 08 Sep 2010 13:35:32 GMT

←Older revision		Revision as of 13:35, 8 September 2010
Line 19:		Line 19:

	If the data are defined as DNA (with Format/DataType, or the command [[nstates]] dna;) the IUPAC nucleotide codes (including polymorphisms) are recognized and used throughout. The states are internally stored as A=0, G=1, C=2, D=3, and gap=4. If the data are instead defined as proteins (with the menus, or using [[nstates]] prot;), the IUPAC codes are recognized and used throughout. For 32 states, non-protein data, the symbols 0-9 and A-V indicate states 0-31. If the data are defined with fewer states, they occupy less memory. This may be necessary for large data sets. The data can also be read as interleaved.		If the data are defined as DNA (with Format/DataType, or the command [[nstates]] dna;) the IUPAC nucleotide codes (including polymorphisms) are recognized and used throughout. The states are internally stored as A=0, G=1, C=2, D=3, and gap=4. If the data are instead defined as proteins (with the menus, or using [[nstates]] prot;), the IUPAC codes are recognized and used throughout. For 32 states, non-protein data, the symbols 0-9 and A-V indicate states 0-31. If the data are defined with fewer states, they occupy less memory. This may be necessary for large data sets. The data can also be read as interleaved.
		+
		+	The possible kinds of characters are:
		+
		+	{Continuous}; {DNA}; {Prot}; {Num}; {Gaps/nogaps}; {trimhead/trimtail}
		+
		+	TNT also recognizes [[Fasta format]].
		+	After that you should include the data.
		+	After the last character and to finish the matrix you should add a semicolon ( ; ).
		+	After the semicolon you can add any setting you desire as command sentences, (e.g. [[outgroup]] = 0).

Manual/Data Input

Sacatalano — Wed, 08 Sep 2010 13:34:53 GMT

←Older revision		Revision as of 13:34, 8 September 2010
Line 7:		Line 7:


-	~~The possible kinds of characters are:~~
-	~~{Continuous}; {DNA}; {Prot}; {Num}; {Gaps/nogaps}; {trimhead/trimtail}~~
-	~~TNT also recognizes [[Fasta format]].~~
-	~~After that you should include the data.~~
-	~~After the last character and to finish the matrix you should add a semicolon ( ; ).~~
-	~~After the semicolon you can add any setting you desire as command sentences, (e.g. [[outgroup]] = 0).~~

	The different blocks may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the block).		The different blocks may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the block).

How to manage several datasets

Sacatalano — Wed, 08 Sep 2010 13:32:49 GMT

New page: The dmerge command merges data files, and saves them as blocks; the character names and settings are also merged (in Windows version, File/MergeDataFiles, using Ctrl+Left Mouse Button ...

New page

The [[dmerge]] command merges data files, and saves them as blocks; the character names and settings are also merged (in Windows version, File/MergeDataFiles, using Ctrl+Left Mouse Button to select multiple files). The [[dmerge]] command also merges (by using * as argument) the characters with identical character names (in Windows version, with Data/MergeHomonymousCharacters). Some basic rules of correspondence between states and state names must be satisfied.

Manual/Data Input

Sacatalano — Wed, 08 Sep 2010 13:32:35 GMT

←Older revision		Revision as of 13:32, 8 September 2010
Line 5:		Line 5:
	==== [[How to manage several datasets]]====		==== [[How to manage several datasets]]====

-	The [[dmerge]] command merges data files, and saves them as blocks; the character names and settings are also merged (in Windows version, File/MergeDataFiles, using Ctrl+Left Mouse Button to select multiple files). The [[dmerge]] command also merges (by using * as argument) the characters with identical character names (in Windows version, with Data/MergeHomonymousCharacters). Some basic rules of correspondence between states and state names must be satisfied.	+

	The possible kinds of characters are:		The possible kinds of characters are:

Alternative formats (Nexus,Fasta)

Sacatalano — Wed, 08 Sep 2010 13:30:54 GMT

New page: The basic features of the '''Nexus''' format are supported in TNT. When parsing a file, if the first string in the file is "#NEXUS" (and the macro language is turned off), then TNT will p...

New page

The basic features of the '''Nexus''' format are supported in TNT. When parsing a file, if the first string in the file is "#NEXUS" (and the macro language is turned off), then TNT will parse the file as a Nexus file. So, you simply open the nexus file in the same way you would open a native TNT file. Some Nexus options are not supported, and then some legal Nexus files cannot be read by TNT; in this case, running the file through PAUP* and exporting the data (e.g. "export file=my_file_name.nex format=nexus interleaved=no") usually produces a file (my_file_name) which can be read with TNT.

The only Nexus blocks that will be read by TNT are those corresponding to data, trees, and assumptions (commands ctype, usertype, include, exclude, and weights). The data can be read in the "dna," "protein" or "standard" formats only (e.g. format datatype = standard;). Unrecognized commands or blocks are simply ignored or skipped. Note that within the NEXUS file, numbering for taxa or characters starts from 1 (one), not from 0 (zero). You can include TNT commands in the nexus file, at the end of the file, preceded by "begin tnt;" (with an end at the end, which is ignored by TNT; otherwise, PAUP* complains that end of file was found when reading a TNT block).

Manual/Data Input

Sacatalano — Wed, 08 Sep 2010 13:30:41 GMT

←Older revision		Revision as of 13:30, 8 September 2010
(6 intermediate revisions not shown.)
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-		+	==== [[Basic format]] ====
-	== [[Basic format]] ==	+	==== [[Alternative formats (Nexus,Fasta)]] ====
-		+	==== [[Continuous characters]] ====
-		+	==== [[Landmark_optimization\|Landmark data]]====
-		+	==== [[How to manage several datasets]]====
-	[[~~Continuous characters]] in TNT can have states 0-65, with 3 decimals~~ (~~thus~~, ~~when not doing [[implied weighting~~]]~~, tree scores are reported always with 3 decimals). The~~ [[~~continuous~~ characters]] must be the first ones in the matrix (i.e. the first block or blocks, followed by blocks with other data formats). Each value must be separated by a blank or space; ranges are indicated by two values separated by a dash (-). Missing entries are indicated only as question marks (?).	+
-		+
-		+
-	~~To see the input format for~~ [[Landmark_optimization\|~~'''landmark~~ data~~'''~~]] go [[~~Landmark_optimization\|'''here'''~~]]	+
-		+

	The [[dmerge]] command merges data files, and saves them as blocks; the character names and settings are also merged (in Windows version, File/MergeDataFiles, using Ctrl+Left Mouse Button to select multiple files). The [[dmerge]] command also merges (by using * as argument) the characters with identical character names (in Windows version, with Data/MergeHomonymousCharacters). Some basic rules of correspondence between states and state names must be satisfied.		The [[dmerge]] command merges data files, and saves them as blocks; the character names and settings are also merged (in Windows version, File/MergeDataFiles, using Ctrl+Left Mouse Button to select multiple files). The [[dmerge]] command also merges (by using * as argument) the characters with identical character names (in Windows version, with Data/MergeHomonymousCharacters). Some basic rules of correspondence between states and state names must be satisfied.
Line 19:		Line 14:
	After the semicolon you can add any setting you desire as command sentences, (e.g. [[outgroup]] = 0).		After the semicolon you can add any setting you desire as command sentences, (e.g. [[outgroup]] = 0).

-	The different blocks may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the ~~block).~~	+	The different blocks may have different taxon composition (i.e. a taxon may not be specified for some block, case in which it is assigned only missing entries for all the characters in the block).
-		+
-	The basic features of the '''Nexus''' format are supported in TNT. When parsing a file, if the first string in the file is "#NEXUS" (and the macro language is turned off), then TNT will parse the file as a Nexus file. So, you simply open the nexus file in the same way you would open a native TNT file. Some Nexus options are not supported, and then some legal Nexus files cannot be read by TNT; in this case, running the file through PAUP* and exporting the data (e.g. "export file=my_file_name.nex format=nexus interleaved=no") usually produces a file (my_file_name) which can be read with TNT.	+
-		+
-	The only Nexus blocks that will be read by TNT are those corresponding to data, trees, and assumptions (commands ctype, usertype, include, exclude, and weights). The data can be read in the "dna," "protein" or "standard" formats only (e.g. format datatype = standard;). Unrecognized commands or blocks are simply ignored or skipped. Note that within the NEXUS file, numbering for taxa or characters starts from 1 (one), not from 0 (zero). You can include TNT commands in the nexus file, at the end of the file, preceded by "begin tnt;" (with an end at the end, which is ignored by TNT; otherwise, PAUP* complains that end of file was found when reading a TNT block).	+

Basic format

Sacatalano — Wed, 08 Sep 2010 13:23:08 GMT

New page: xread 'optional title, starting and ending with quotes (ASCII 39)' nchar ntax Taxon0 1011110000 Taxon1 1111111000 Taxon2 1011110000 Taxon3 1111111000 ; ...

New page

[[Commands/xread|xread]]
'optional title, starting and ending with quotes (ASCII 39)'
nchar ntax
Taxon0 1011110000
Taxon1 1111111000
Taxon2 1011110000
Taxon3 1111111000
;

[[xread]] is the command to read the datamatrix. After that, in the following line you should include a line with the number of characters and the number of taxa. After that you should include the dataset itself, finishing with a semicolon.

By default taxon names must have up to '''32 characters'''. The command [[taxname]] allows to change this value to any number.

Taxon names must not contain the following characters: semicolon (“;”), slash (“\”), or plus and minus (“+” “-“ ), or any white space (tab or space).

After the name and separated by a space start the characters.

Always, in TNT, the '''first character and first taxon are referred to as number 0'''. Polymorphisms can be entered by enclosing the state(s) in square brackets. By default, up to 16 states are allowed by [[xread]], using symbols 0-9 to indicate states 0-9, and A-F to indicate states 10-15. This can be changed with the [[nstates]] command, which defines the number of states (and data type) to be subsequently read; using the menus, this can be changed with Format/DataType.

If the data are defined as DNA (with Format/DataType, or the command [[nstates]] dna;) the IUPAC nucleotide codes (including polymorphisms) are recognized and used throughout. The states are internally stored as A=0, G=1, C=2, D=3, and gap=4. If the data are instead defined as proteins (with the menus, or using [[nstates]] prot;), the IUPAC codes are recognized and used throughout. For 32 states, non-protein data, the symbols 0-9 and A-V indicate states 0-31. If the data are defined with fewer states, they occupy less memory. This may be necessary for large data sets. The data can also be read as interleaved.

Manual/Data Input

Sacatalano — Wed, 08 Sep 2010 13:22:53 GMT

←Older revision		Revision as of 13:22, 8 September 2010
(One intermediate revision not shown.)
Line 1:		Line 1:
-	~~The basic~~ format ~~for data input is:~~	+
		+	== [[Basic format]] ==
		+

-	~~[[Commands/xread\|xread]]~~
-	~~'optional title, starting and ending with quotes (ASCII 39)'~~
-	~~nchar ntax~~
-	~~Taxon0 1011110000~~
-	~~Taxon1 1111111000~~
-	~~Taxon2 1011110000~~
-	~~Taxon3 1111111000~~
-	;
-
-	[[xread]] is the command to read the datamatrix. After that, in the following line you should include a line with the number of characters and the number of taxa. After that you should include the dataset itself, finishing with a semicolon.
-
-	~~By default taxon names must have up to '''32 characters'''. The command [[taxname]] allows to change this value to any number.~~
-
-	Taxon names <span style="color:red; font-weight: stronger;">must not contain</span> the following characters: semicolon (“<span style="color:red;">;</span>”), slash (“<span style="color:red;">\</span>”), or plus and minus (“<span style="color:red;">+</span>” “<span style="color:red;">-</span>“ ), or any white space (tab or space).
-
-	~~After the name and separated by a space start the characters.~~
-
-	Always, in TNT, the '''first character and first taxon are referred to as number 0'''. Polymorphisms can be entered by enclosing the state(s) in square brackets. By default, up to 16 states are allowed by [[xread]], using symbols 0-9 to indicate states 0-9, and A-F to indicate states 10-15. This can be changed with the [[nstates]] command, which defines the number of states (and data type) to be subsequently read; using the menus, this can be changed with Format/DataType.
-
-	If the data are defined as DNA (with Format/DataType, or the command [[nstates]] dna;) the IUPAC nucleotide codes (including polymorphisms) are recognized and used throughout. The states are internally stored as A=0, G=1, C=2, D=3, and gap=4. If the data are instead defined as proteins (with the menus, or using [[nstates]] prot;), the IUPAC codes are recognized and used throughout. For 32 states, non-protein data, the symbols 0-9 and A-V indicate states 0-31. If the data are defined with fewer states, they occupy less memory. This may be necessary for large data sets. The data can also be read as interleaved.

	[[Continuous characters]] in TNT can have states 0-65, with 3 decimals (thus, when not doing [[implied weighting]], tree scores are reported always with 3 decimals). The [[continuous characters]] must be the first ones in the matrix (i.e. the first block or blocks, followed by blocks with other data formats). Each value must be separated by a blank or space; ranges are indicated by two values separated by a dash (-). Missing entries are indicated only as question marks (?).		[[Continuous characters]] in TNT can have states 0-65, with 3 decimals (thus, when not doing [[implied weighting]], tree scores are reported always with 3 decimals). The [[continuous characters]] must be the first ones in the matrix (i.e. the first block or blocks, followed by blocks with other data formats). Each value must be separated by a blank or space; ranges are indicated by two values separated by a dash (-). Missing entries are indicated only as question marks (?).

TNT updates

Sacatalano — Wed, 08 Sep 2010 13:09:09 GMT

←Older revision		Revision as of 13:09, 8 September 2010
Line 1:		Line 1:
		+	'''Fixes/changes to the version of June, 2010 (August, 2010)'''
		+	* Added option to save tree-diagrams as Scalable Vector Graphics (SVG) files. These can be opened with almost any web browser, as well as other graph-manipulating programs. This saves only the tags copied with the “multiple tag storing” (set with ttag=;), and is a new option of the ttag command (see help ttag;). The tags can be saved as color figures (i.e. coloring tree-branches) or black-and-white diagrams. Thanks to Salvador Arias (who first implemented some of this as a TNT script) for showing me how to do this with XML code.
		+
		+	----
		+
		+	'''Fixes/changes to the version of March, 2010 (June, 2010)'''
		+
		+	* there were problems with character-state trees, both with tree-length calculations themselves (due to problems with internal binary recoding), and with the fit expression for individual characters (the expression calculated the fit for the character-state tree as a whole, instead of using the sum of fits for the binary variables representing the character, producing an inconsistency with values reported by searches or for the entire tree). [Martín Ramírez]
		+	* Added the option to calculate the fit for character-state trees as units, under implied weighting, instead of decomposing them in binary variables.
		+	* Added option to read group names in scripting expressions. Also added expressions $agroup, $tgroup, $xgroup, and $hgroup.
		+	* Typing the wrong [topic] for help could crash the program. Fixed. [Jan De Laet ]
		+	* Linux/Mac only: Improved the way in which the program accesses the home directory to read/store password (after accepting license terms) and command history. Before, the program did this by means of a temporary file created in current directory, which could create problems if the user was running TNT in a directory without write permissions. Jan De Laet provided me with more proper code (thanks!), so that keeping track of acceptance of license terms and command-history are now cleaner. [Jan De Laet]
		+	*A bug introduced in Feb. 2008 (with the faster tree-sorting operations) but discovered only recently: calculating pruned consensus (prunnelsen, or Trees/Comparisons/PrunedTrees) could produce bogus results or output. This happened only when displaying the results, not when simply saving pruned trees to memory. This was because some tree-simplifying operations done when pruning made the trees intractable by the new tree-sorting routines. Fixed.
		+	* Depending on the set of input trees, reduced the amount of memory needed to calculate SPR differences between large trees (sprdiff). In many cases, the algorithm is also about 30% faster.
		+	* Last minute fixes to the June version: some of the previous fixes created problems for many character-mapping options under implied weights. The version with this problem was up in the web for about 10 days. If you downloaded it before, and sometimes use implied weightng, make sure you get the replacement version. Also fixed a long standing (but yet undiscovered) bug in calculation of scores under implied weights, for step-matrix characters that were actually equivalent to Fitch characters with weight greater than unity –this led to miscalculations of tree-scores during searches.
		+	* Mac 64 bits only: fixed a long standing (but previously undiscovered) bug, when printing tables (and possibly other kinds of output) with numbers having decimals (e.g. implied weighting scores, length with continuous characters included).
		+
		+	----
		+
	'''Fixes/changes to the version of January 2010 (March, 2010)'''		'''Fixes/changes to the version of January 2010 (March, 2010)'''
	* Windows only: in the dialog for Optimize/CountSpecificChanges, selecting “all trees” after having selected some trees did not actually optimize all trees –it used the previous tree-selection again. Fixed.		* Windows only: in the dialog for Optimize/CountSpecificChanges, selecting “all trees” after having selected some trees did not actually optimize all trees –it used the previous tree-selection again. Fixed.

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	===[Ranges]===		===[Ranges]===
-	For any command that takes ranges, two numbers separated by a period (X.Y) indicate a range	+	For any command that takes ranges, two numbers separated by a period (X.Y) indicate a range
-	(from X to Y, inclusive). A blank space before the period indicates that the range starts	+	from X to Y, inclusive). A blank space before the period indicates that the range starts
-	from the first possible value, and a blank after indicates that the range ends in the last	+	from the first possible value, and a blank after indicates that the range ends in the last
-	possible value. Note that names cannot be separated by a period to indicate ranges. Except	+	possible value. Note that names cannot be separated by a period to indicate ranges. Except
-	for the ccode command (where they have a special meaning), the + (or – ) symbols indicate	+	for the ccode command (where they have a special meaning), the + (or – ) symbols indicate
-	inclusion (or exclusion) from the list.	+	inclusion (or exclusion) from the list.
	----		----
	===[Groups]===		===[Groups]===
-	Up to 32 groups of trees, characters, and taxa can be defined. After having defined a	+	Up to 32 groups of trees, characters, and taxa can be defined. After having defined a
-	group, enclosing in curly braces ({}) the group number (or name, if named) is equivalent	+	group, enclosing in curly braces ({}) the group number (or name, if named) is equivalent
-	to specifying each of the members of the group. For taxon specifications, using @X Y refers	+	to specifying each of the members of the group. For taxon specifications, using @X Y refers
-	to all the terminals included in node Y of tree X; under Windows versions, the equivalent	+	to all the terminals included in node Y of tree X; under Windows versions, the equivalent
-	is accomplished by selecting nodes under tree-viewing mode (Trees/View). For character	+	is accomplished by selecting nodes under tree-viewing mode (Trees/View). For character
-	specifications, using @X Y Z refers to the Yth and Zth characters in block X (note that Y	+	specifications, using @X Y Z refers to the Yth and Zth characters in block X (note that Y
-	and Z can themselves be ranges	+	and Z can themselves be ranges
	----		----

	===[Blocks]===		===[Blocks]===
-	If the data contain blocks, the first one is numbered as 1, and block 0 refers to the entire	+	If the data contain blocks, the first one is numbered as 1, and block 0 refers to the entire
-	set of characters. The blocks can be referred to by their names (if defined); the name "all"	+	set of characters. The blocks can be referred to by their names (if defined); the name "all"
-	is always used for the entire matrix. If the data are read as interleaved, the blocks of data	+	is always used for the entire matrix. If the data are read as interleaved, the blocks of data
-	are automatically preserved (although they can be changed with the blocks command). Within	+	are automatically preserved (although they can be changed with the blocks command). Within
-	execution of a given command, the @X for characters remains in effect until deactivated	+	execution of a given command, the @X for characters remains in effect until deactivated
-	explicitly with @0 or @all.	+	explicitly with @0 or @all.