TNT updates

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

  • Windows only: fixed glitches with the behavior of the new report window, and with the focus after execution of some command (this had been changed with the last version, it now behaves more like before, automatically going back to command line without the need of using the mouse).
  • Added option to extrapolate user-defined weighting functions for weighting-sets (both with a unique concavity, or extrapolating to missing entries).
  • Fixed some minor problems here or there with the interpolator (it had some tendency to freeze or take too long, for some specific curve shapes).
  • There were problems calculating minimum possible numbers of steps for continuous characters with lots of polymorphisms [ Bruno Mederos ]
  • The commands for realigning landmark configurations are now more stable, and include the tree-based alignment algorithm by Catalano & Goloboff (in press, Syst. Biol.). Most of the code for aligning landmarks was written by S. Catalano.

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

  • The extrapolator (used for extended implied weighting under user-defined weighting functions, and for the intpol scripting expression) could sometimes freeze (or take a very long time to produce calculations).
  • Windows versions, running under VISTA: there were problems (which I hadn't seen myself, not having a machine with Vista) with reporting progress of searches and time-consuming operations. The program stopped responding, and searches could not be interrupted. This should work now. I have not so far been able to make the “pause” button work properly under Vista, reason for which I hve made it optional (to enable pausing, which works under XP, type “pause[;” at the command line).
  • Added the “!” option of the tcomp command, which calculates the PCR index (Pol & Escapa, 2009) for the specified taxa. This is intended to facilitate calculation of PCR (it is much faster than the original implementation using scripts, and can handle much larger cases). There is also work in progress, in the PCR command, but this is not yet documented.
  • A few cosmetic changes here or there.

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

  • Now all versions (Windows included) write to log file (if open) the version number and date, as well as OS. [ David Maddison ]
  • Added the possibility to save HTU's together with the matrix (by specifying a tree to use for reconstructing the HTU's, see online help for xread).
  • Changed the behavior of the keepall option of the xmult command; now, when doing more than one hit to the best length, keepall retains the trees resulting from the fusing of the initial replications. Together with noupdate, this can be used to save the trees resulting from each set of replications (e.g. xmult = hit 5 noupdate keepall).
  • Now the color of tree-branches in “tree-tags” (ttag command) can be specified (on a branch-per-branch basis) as RGB color codes (in parentheses, separated by commas). You can also specify branch thickness (as a fourth number within the parentheses). This is used when saving tree-diagrams as SVG files in all versions, and in the windows versions (where the branch color/thickness can be changed, when the tree is unlocked, by double right-clicking on the node and entering the RGB color and thickness).
  • Linux/Mac versions: now it is possible to obtain help for each command by typing "command ?” (this used to be available only for Windows versions).

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

  • Parallel versions only: fixed problems deciding RAM in slaves in 32-bit versions; better estimation of amount of RAM needed in slave.
  • Parallel versions only: setting number of tree-groups to other than 32 crashed slaves. Fixed now.
  • The command hybrid often crashed the program; now the two trees can be given as a scope (or tree-group).
  • Parallel versions only: improved the behaviour of launching new jobs in clausters with slow communication. Before, launching a job with many tasks for a big data set could overload pvm daemons; the use of communication at that initial stage is now more parsimonious. Also, improved the speed with which slaves can communicate for many tasks.
  • Running under implied weighting some sankoff characters with more than 16 states, or sankoff characters with any number of states on versions with no limit on the number of taxa, produced internal errors (and a message warning about score miscalculation). Fixed now.
  • Large data sets required a lot of RAM to run under implied weighting, most of which was needed for buffering steps under tree-fusing. If the amount of RAM allocated is too low for tree-fusing under implied weighting, tree-fusing is simply disabled, but the rest of the searches can be carried out.
  • Added options for “extended implied weighting.” This allows defining sets of characters with constant weight, sets of characters to be reweighted according to group homoplasy (instead of individually), and different weighting strengths for different characters (including the possibility of taking missing entries into account, extrapolating from homoplasy in observed entries to missing entries). This is a complex option (it took a month of intense programming), so it may have some glitches here or there. See details with “help xpiwe;”.
  • Improved the behaviour of recursive sectorial searches on several fronts (now including, in parallel versions, the possibility of launching slave jobs from within the sectorial search).
  • Last minute fix to the update: SPR differences (after changes introduced june, 2010) typically produced meaningless values when moves needed to produce/resolve polytomies were counted. Fixed now. [ Brian Andres ]

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)

  • 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.
  • The maximum length of taxon names is now also used for the maximum length of tree-tags (if larger than 128).
  • There was a memory leak when naming loops; if the loop was repeated a large enough number of times, then this may have caused out-of-memory problems that shouldn't have been there. Fixed now. [ Salvador Arias ]

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

  • Added the grptogrp (=group-to-group) expression to the scripting language.
  • A few really minor/cosmetic changes.

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

  • There was a bug, unlikely to be noticed by users, which made sectorial searches use “combined strategies” (as in gocomb) when no value for gocomb had been set by the user and the sector selected was large enough to be analyzed with tree-drifting. This did not affect searches that defined a sector size above which to use combined strategies, and it did not affect searches with user-defined algorithms for each sector.
  • Some specific combinations of sector sizes with exclusive sector selections may have caused memory problems which resulted (most likely) in crashes. This could happen only for relatively large sectors (almost half the taxa). This is fixed, and it is now possible to run exclusive sector selections dividing tree in 2 pieces (minimum used to be 3).
  • Added the option to reroot tag-tree, and to specify an internal node as rooting point (see online help for reroot).
  • Parallel versions only: an unlikely problem: when running some resampling in slaves, but not using any actual search routine to analyze each data set (yeah, right!), there were problems if the results were spied with ptnt spy (ptnt get worked ok). Spying should be ok now.
  • Problems could also have arisen after resampling using the low-memory consensus algorithms (probably needed for very large data sets), when some taxa had been deactivated. Fixed now.
  • For very large numbers of taxa, the speed of the low-memory majority rule consensus algorithms has been vastly improved.
  • Improved the way in which initialization of the program is carried out in Linux and Mac when it is run for the first time (people using Mac were specially adept at screwing up when installing).

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

  • The command chomo (character homoplasy) was supossed to take a list of trees as argument, but it didn't –it always did all trees. [ Salvador Arias ]
  • Windows only: saving data for “only active characters” (Data/saveData) saved block definitions for the original matrix (i.e. the matrix with all characters) with a blocks command at the end of the file. This block definition was incorrect, and unnecessary, since the data were saved in proper blocks (thus, reading the matrix naturally produced the right block definitions). The blocks command at the end of the file is now skipped when saving only active characters. [ Mark Siddall ]
  • Renaming characters but without naming the states created bogus names for states. States remain unnamed now.
  • Windows versions only: improved the aesthetics and cosmetics (if not the ethics) of the display for landmark mapping.
  • Improved and added new options for re-aligning landmark data; see help for the lmrealign command (also added menu options for realigning, under Data/Landmarks). The tree-guided algorithms provide the best fit for the tree used as guide, using a method by S. Catalano and P. Goloboff (in prep.). The code for alignment was written in collaboration with S. Catalano.
  • Windows versions only: added to the menus some options for landmark optimization, under Settings/LandmarkOptimization, and the possibility to call the mapper for landmarks from the menus (under Optimize/Characters/Landmarks).

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

  • Calculation of branch lengths was totally screwed up when there were sankoff characters. They're ok now. [ Diego Pol ]
  • The sprit or tbrit commands could cause crashes or freezes (I believe, after changes introduced March, 2009).
  • It is now possible to re-align 2D landmark data using RFTRA. The code for this (not stable yet!) was written mostly by Santiago Catalano.
  • When naming loops, all letters were downcased, but when subsequently accessing loop values the name was not. This caused unexpected errors if you attempted to name a loop with upper-case letters –loop values could subsequently be accessed only using lower case. Loop name is now read in lower or upper case (and continues being accessed in the same way). [ Salvador Arias ]

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

  • The rfreqs command did not properly handle elimination of some taxa. It does now.
  • Changed the way in which similar groups in trees are recognized (macro expression simgroup, and rfreqs command). The new way uses a lot less memory (previous algorithm needed roughly an extra 3T2/4 bytes for T taxa, while the new algorithm uses only 16T extra bytes in the case of versions with no limit in the number of taxa, 8T otherwise –for the 73,060-taxon data set of Goloboff et al. 2009, this is over 4 GB instead of only 1.2 MB), and is a lot faster (for 500 taxa, 20 to 1, for 2500, 80 to 1, for 13000, 300 to 1). This means that the scripts used by Goloboff et al. (2009) in their eukaryote paper, can now be used on a windows machine, allocating only 1.5 GB of memory.
  • Given the above, the view command was added to Windows versions, but only with the “search” option (i.e. view : xxx; positions the cursor at the next occurence of string “xxx”).
  • A strange bug occured in some unusual circumstances during searches, when the nuber of rearrangements examined had a certain number of digits. This was due to a bug in the function that writes the number of rearrangements examined, and only under 32-bit Linux were any effects detected. The bug caused unstable/erratic behavior during or after the search, and may have caused crashes as well. This is fixed now. [ Rafael Miranda ]

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

  • when a landmark comprised only identically positioned points, the (default) noinscale option produced correct results, but the inscale option produced erroneous cost calculations (even when the cost contribution for the landmark was 0). This is fixed now.
  • Landmarks with a missing entry in the outgroup caused all sorts of problems (miscalculations, etc.). Fixed now.
  • Added the options termpoints and options to the landmark command (see help command).
  • Windows versions only: when running landmarks, now it is possible to better place the tree on screen if the (default) auto-shift of wide screens (under Format/DisplayBuffer) is turned off.
  • Parallel versions only: running the ptnt command from within a tbrit or sprit loop caused (after changes to sprit and tbrit done in March, 2009) problems with the memory management for the macros. It can be run ok now.
  • Versions with no taxon limit (whether 64 or 32 bit): the option to map a character on several trees at a time (map [, or Optimize/Characters/CommonMapping) produced erroneous output. Fixed now [ Martín Ramírez ]
  • The travtree command had problems on trees with many polytomies (versions with no taxon limit were more prone to the problem). Fixed now. [ Diego Pol ]

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

  • Running resampling with xmult and/or sectsch for small data sets (20 or fewer taxa) sometimes caused crashes. This is really not something people were expected to do (running such small data sets with those routines is an overkill), but it should have worked anyway. Fixed now.
  • On some rare ocassions, data sets with continuous characters may either have (a) interrupted searches and displayed an error message about an "internal error in TBR calculations", or (b) never finished searching, although the search could be interrupted and had the appearance of working normally. This seems to have been more likely to occur under Windows, due to code changes made by the compiler to my code during optimization.
  • Added the maketables + option, to save in an array the values displayed in a table.
  • The parsing of definitions of positive and negative constraints sometimes didn't work properly (in either Windows or other versions).
  • Some options for analyzing landmark data are now ready for use. See help lmark. For the time being, landmark data can be mapped onto trees, but no tree searches are implemented in TNT. Searches can be implemented only in combination with the scripting language (see here for some scripts). Added several macro expressions (lmscore, lmwt, lmfactors, lmnchar, lmnpoints), useful to handle landmark data.

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

  • Made the track option of sectsch more stable .
  • Parallel versions only: couldn't run sectors when some taxa were deactivated. It works ok now.
  • Fixed a few problems with the landmark stuff (but this continues being in pre-beta).
  • Slightly changed the way in which existing tree-tags are handled when doing recursive sectorial searches
  • Added the DSS option to the sectsch command, and (for parallel versions only) the "sector D" option to the ptnt command. This option provides an easy way to effect a sectorial search around a node specified by the user.
  • When renaming chars., a blank before the semicolon caused an additional state to be named " " (blank). Only real strings used now.
  • Added option to collapse user-specified nodes to the condense command.
  • Scripting: vastly improved speed for the expression eqgroup in large data sets.
  • Parallel versions only: the sprit and tbrit commands could not be run in slaves. They can now; now they silence the output automatically (as in travtree or recursive sectorial searches).
  • Parallel versions only: the treeparts expression may have miscalculated number of parts if no search had been done before.
  • Re-inserting duplicate taxa into tree(s) caused the program to crash. This was introduced in previous version, with the possibility of reinserting taxa into tree-tags (which worked ok; only actual trees caused problems).
  • Added “help topics” (i.e. help [ topic ] displays all commands for topic topic).

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

  • Reading trees with excess/unbalanced parentheses caused the program to abort reading trees; the program now tries to fix the trees.
  • This version includes some work in progress, on landmark data (unstable and unfinished; missing entries cannot yet be handled). This is mostly undocumented; future versions (and a paper) will document it properly.
  • Windows versions only: it should now be possible to double-click (or drag-and-drop) files saved in folders with spaces in the names!
  • Linux versions only: added the option to replace the instructions for TNT when it is running in the background. If the file tnt_execute_PID (where PID is process ID of the TNT instance to reset) exists in current directory, then when TNT runs out of instructions –or finds a quit command, or file stop_tnt_PID exists in current directory (see additions to version of November 2005)- then TNT begins taking input from file –renaming it as a new file, so that instructions can be replaced again. With this (pause_tnt, stop_tnt, and execute_tnt) the user can have complete control of a TNT process running in the background.
  • Running constrained sectorial searches (CSS) with user-defined tree constraints in which there was a (large) basal polytomy caused bogus results, crashes or freezes. This is fixed now.
  • Relative fit differences when TBR-collapsing during implied weighting may have been miscalculated (underestimated). This error is unlikely to have been noticed, except by someone who was paying very close attention to the results.
  • Added the option to calculate bremer supports by keeping track of the score differences during TBR swapping. This is the “!” option of the bsupport command. This is probably the best way to estimate bremer supports for very large data sets. To my knowledge, the only program which has implemented this method is POY (versions 3 and 4). The implementation in TNT differs from POY's in that TNT can swap several trees (keeping track of the score differences among the source trees themselves), it can ignore the positions of selected taxa, and it can calculate relative bremer supports in addition to absolute supports.
  • Added the track option to the sectsch command, as well as the macro expressions nodtosect, biginsect, bignotsect, and bigntax. These should allow calculating approximmate support values from analyses of sectors of the tree. NOTE: For running TNT in parallel, this addition means that the slaves must be updated, too, or they won't be able to receive the data from the master.
  • The riddup command (to eliminate or reinsert duplicate taxa) is now, for large data sets, orders of magnitude faster.
  • The reactivating/reinserting option of the riddup command (riddup - ) may have altered node numbers for the trees (so that node numbering did not follow the same standard as all other TNT command).
  • Added the “/ ” option to the riddup command, to reinsert duplicate inactive taxa into the tag-tree. This can be used to calculate supports with duplicates deactivated and store them in tags; subsequent re-insertion of the duplicates into the tree shuld not change the support values.

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

  • Defining positive or negative constraints, and then changing the number of maximum trees, produced freezes or crashes (note that changing number of max. trees first and then defining the constraints should have produced no problems). This is fixed now. [Martín Ramírez]
  • Windows only: defining from the menus negative constraints, or positive constraints with some floating taxa, caused an internal error message. The constraints could thus be defined only by using commands. Fixed now. [ Julián Faivovich ].
  • Running multiple random addition sequences under implied weights, accepting suboptimal trees caused crashes (and, possibly, unexpected bahviour). Running multiple random addition sequences accepting suboptimal trees is generally undesirable (except under very specific circumstances, e.g. running few replications saving many trees each); however, one expects it to function. The problem was because the value of maximum score acceptable during a replication depended on the score of the best tree found so far (i.e. in previous replications) and the value of suboptimal. This meant that, sometimes, a tree which improved the score during a replication was nonetheless “unacceptable”, causing further problems. Now, the maximum acceptable score for multiple random addition sequences under implied weights is determined by the best tree in that replication alone (when not using implied weighting, it continues being, as before, the best tree so far). [ Martín Ramírez ]
  • Linux 64-bit versions only: re-setting maxtrees to a large number when character names had been defined either crashed the program or issued an error message stating that not enough RAM was available (when in fact it was). Fixed now.
  • Linux 64-bit versions only: several error or notification messages could have potentially produced bogus output –don’t know whether this actually happened to anyone. It’s safe now.

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

  • Windows versions only: added option to contract the trees (in the pre-viewing screen) so that the entire tree fits the screen (this makes it possible to look at very large trees). To toggle this, press "f". Taxon names may overlap when doing that and it may be better to use color mappings to indicate groups; in this case, taxon names may be hidden by pressing "n" (also a toggle). If taxon names are hidden, a single left-click on a node toggles display of the name of that taxon (or its descendants). To move the tree by small steps, use "k" and "l".
  • Searches under tree-constraints could crash the program when (1) there were pre-existing trees in memory, and/or (2) no tree-searches had been done before.

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

  • The parsing of long matrices with multiple data blocks was very slow (due to the addition, in the previous version, of the match option, which allows for application of the Needleman-Wunsch algorithm to taxon names; note that now all letters after a cuadruple underscore are ignored). The parsing is now as fast as it was before.
  • The verbose option as specification for a block (within square brackets) was added.
  • Very long group names (i.e. within the length specified with taxname+, but over the previous limit of 32 characters) could cause errors (or possibly crashes).
  • Added the int option to the bbreak command. This option uses a special kind of sorting for the characters to be optimized during swapping; option 1 considers only the most relevant characters, option 2 re-orders them, so that the most relevant are checked first (often requiring examination of fewer characters). These two options are useful only for very large data sets (>10,000 taxa) with many characters.
  • Windows only: attempting to swtich to tree-viewing mode without enough memory available to optimize a tree crashed the program. The program now attempts to recover more gracefully from that [Santiago Catalano].
  • Parallel versions only: improved memory management and speed for recovering trees (with either spy or get) from sectorial searches in parallel. Also improved memory management in a couple other places.
  • Added the option to never make space for assigning costs to Sankoff characters. When characters are read as 32-states this can save a small but yet significant amount of memory (see help costs).
  • Fixed potential crashes (or erroneous calculations) with TBR under sectorial searches (specially likely to cause problems with recursive sectorial searches).
  • In 64-bit versions with no taxon limit, trying to open a file for saving trees for more than 16,383 taxa in compact format and append mode caused an improper error message to be displayed. Fixed.
  • A bug introduced in the April, 2008 version: the prunnelsen command (Trees/Comparisons/PrunedTrees) crashed (or produced bogus results) when input trees had polytomies (and perhaps under other circumstances). This was because the faster tree-sorting, which had a problem for sorting reduced trees.
  • Added possibility to not prepare memory space for sankoff costs when reading the data. For data sets with many characters and many states, this can save a small (but significant) amount of memory, if you do not plan to use step-matrix characters.
  • Improved memory usage of recursive sectorial searches in master process (which formerly allocated some amount of unnecessary memory).
  • Fixed some glitches with prediction of number of clusters for reduced data sets during sectorial searches.
  • A bug which could have caused errors in either sectorial searches, or any search in which some taxa had been deactivated (either causing TNT to crash, or to miss some TBR rearrangements), was fixed.
  • Compact tree files for more than 16383 taxa in append mode could not be opened. They can now.
  • Testing of monophyly (hard constraints) for searches in very large data sets is now much faster.
  • Sectorial searches for cases where no character had less than 9 states, but sector ended up having some characters with 8 states or less, often asked for inordinate amounts of slack, too large to satisfy. Fixed.
  • Report of "more slack required" informed of the increase over current setting; it should have said:

"... 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.

  • Sectorial searches for cases with lots of characters with different prior weights, and with some 9-32 state chars which became 8-state or less for the sector, produced problems (messages of internal errors or undetected erroneous length calculations). Fixed. [Mark Siddall]
  • Sectorial searches for cases where matrix had some 32-state characters and no 16-state, but sector ended up having some 16 states, caused crashes. Fixed

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

  • It is now possible to read and save FASTA files. Reading: "proc & file". If file starts with =N, then it fills with gaps (the same effect is achieved with =N after the &). Saving: export ! filename (use !! to skip gaps).
  • Maximum length of taxon names now can be changed, with "taxname +N". This has to be done before reading the data set. In the case of Linux/Mac, this change makes the new binaries incapable of communicating with old binaries when running in parallel: make sure you update slaves!!
  • It is now possible to plot polytomous trees more symmetrically than before. See help for tplot.
  • For data in multiple blocks (xread format only), it is now possible to have a loose checking for name matches (with [match S], where S=similarity), using a Needleman-Wunsch algorithm to calculate distances (similarity is obtained dividing edit cost by length of shortest sequence and subtracting the result from 1).
  • Now string conversions (including $taxon, $character, etc.) can use the part of the string that comes after (>) or after (<) a given symbol x. To do this for taxon N: $taxon <x N. They can also use the first C characters in the string: $taxon:C N (if C is negative, then it uses only the last C characters; if C preceded by a + sign, then it uses the characters beyond C). If C is greater than the length of the string, then it adds blanks (after –in the case of a negative C, before- the string itself).
  • Fixed some potential problems with the mxproc command (commands following it sometimes were not properly parsed), and with displaying of error messages from within loops (which sometimes caused crashes).
  • Scopes of essentially any kind, can now also select things for which the string provided appears somewhere. For this, precede the string with a colon. E.g. if a taxon is called Xus_yus, then "taxcode - :yus;" will deactivate that taxon. This can be used when the names contain some taxonomy. Suppose taxon names are:
    • 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.

  • The tread command now can read taxon groups. For very large data sets (i.e. over 10,000 taxa), speed was vastly improved in many operations which require tree-sorting.
  • Searches could in some rare cases be terminated with a message of an internal error in memory allocation. This is less likely now.
  • Windows only: under auto-weighted optimization, attempting to switch to tree-viewing mode when a tree was polytomous caused the program to exit. Fixed now.
  • Now it is possible to condense trees (condense command) excluding some taxa.
  • Low memory algorithms are now also available for majority rule consensus (majority command); in addition to consuming less memory, the new algorithms sometimes are (for large data sets) faster than the previous (default) ones. This is set with nelsen <;. One limitation of these algorithms is that taxa cannot be ignored during consensus calculation, and trees cannot be collapsed temporarily (thus the addition of the previous option to the condense command, to physically collapse trees and exclude taxa).
  • It is now possible to truncate long taxon names on output to N letters, with the taxname [ N option (use taxname ] to output complete name).

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

  • Saving pruned trees (prunnelsen command, or Trees/Comparisons/PrunedTrees) sometimes caused freezes (and, conceivably, crashes). This seemed more likely when some taxa were excluded a priori, but it may have happened as well under other circumstances. Hopefully fixed.
  • Resampling under TBR-collapsing, when the outgroup was not the first taxon in the matrix, corrupted the results. Fixed now.
  • There were problems when the autosave option was used during sectorial searches (the trees saved to file were corrupted). Fixed now. [ David Maddison]
  • The handling of multiple tree-tags (which used to often cause problems) is now cleaner.
  • Running searches (or sometimes, even optimization of a given tree) under auto-weighted optimization with some sankoff characters caused problems. Fixed now.
  • Trees were sometimes not properly put into tree-groups after the user had re-defined (manually) some tree groups. Fixed.
  • Windows only: Excluding taxa from the strict consensus and showing their location on the tree, using the menus, did not group taxa which belong to a single node in the consensus (as done if using commands). They are grouped now

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

  • The program now is free. The password system is changed, and (in Windows version) it is now possible to run the program even if you have no administrator rights.
  • Some potentially unsafe memory reallocations were changed.
  • Fixed problems with indicating location of pruned taxa on the consensus when input trees had different taxon sets.
  • Added 64-bit Linux versions, and the possibility of running any number of taxa (before, no more than 16383 could be analyzed). The version that can run more than 16383 taxa uses more memory to store the trees (as 32-bit ints, instead of 16-bit ints). In 64-bit machines, this shouldn't be a problem.
  • The option of the xread command that generates data under a simple JC model now can take two decimals for the probability of stasis. Before, the highest possible probability of stasis was 99; now, it's 99.99.
  • Parallel versions only: it is now possible to specify the number of jobs to spawn on each slave (to be used when some machines are faster, or have more than a single processor). See online help for the ptnt command.
  • Fixed some potential problems when reading groups of taxa or characters (or hosts, in parallel versions): groups beyond 31 could be accepted in some contexts, even of those groups could not be defined).
  • Added possibility to use branch-lengths defined by the user to the option for generating data (see online help for xread).
  • Converting a string used to add a white space right after the string. This was annoying under many circumstances [Diego Pol]. No white space is added now.
  • Comments embedded within instructions for iterrecs and travtree are now not counted (maximum is now 4128 bytes of actual commands).
  • Added the wcluster option, which makes wagner trees for very large data sets up to 3 times faster (see on-line help for mult). This is of no use for data sets below 1000 taxa.
  • Plotting synapomorphies common to several trees, while correct in itself, sometimes caused subsequent tree-mappings to be incorrect.
  • Added the option to not use memory for identifying nodes to shrink (which, in large data sets, can be a significant amount of memory). This is set with tshrink! (i.e. exclamation mark) before reading the data set.
  • Added option to calculate strict consensus trees, and to compare trees (tcomp command) using algorithms which consume very little memory (and which, in the case of the strict consensus, are sometimes faster than the previous one). When free memory is low, these algorithms are used automatically; their use can be forced with nelsen< (the default is using low mem algorithms only if memory is low, set with nelsen>).

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

  • If the transformation cost between two states in a step-matrix character equalled 0, and implied weighting was ON, the program could not calculate tree-scores during searches. This was because of the formula used to calculate to calculate fits for sankoff characters, which uses the minimum possible cost. The "minimum possible" for characters where some transformations cost 0 (which continue being unexpected and may produce problems in other fronts!) is now considered as unity, so that the score calculations under implied weighting are "correct". [ Santiago Catalano ]
  • Added the hifile command for scripting, which allows handling input files. See "help hifile;" for details, and associated expressions hifchar, hifstring, hifeof, hifline, hifnumber, hifspy.
  • If the tree order had been just randomized (command "randtrees/;"), some search command sometimes failed to find all equally parsimonious trees. This was because of a bug which made TNT think that additional most parsimonious trees were duplicates of preexisting trees, when they were in fact different. Exact searches did not place their trees in a tree-group;

now they do, in a group called "exact_search".

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

  • Program initialization can now be done similarly in the Mac/Linux/Windows version, with a unique password system.
  • The commands that show reduced trees (resols, prunnelsen) did not use the tree-shrinking definitions. Now they do.
  • Under exclusive sectorial searches, with sectors analyzed with a combined strategy (gocomb option), if the number of starts (combstarts) was greater than twice the number of starts defined for smaller sectors (starts), the program crashed. Fixed now.
  • Sectorial searches under auto-weighted optimization, when recording to text-buffer search status every few seconds, often displayed/saved the wrong scores (this was because the score was displayed/saved for trees during intermediate stages of the search). This is fixed now.
  • Running under implied weighting using internal steps could create problems under two situations: (1) if some additive character with uninformative state(s) was assigned internal steps, the scores reported for a search (any search) did not agree with those for a subsequent optimization (this was due to a constant difference, so it did not affect results, but it was annoying); and (2) if some continuous character had been assigned internal steps, tree scores under sectorial searches could be wrong (usually considered lower than they truly were). These two are fixed now. [Claudia Szumik]
  • Linux/Mac versions only: when running in the background, some commands to clear the screen were not ignored, which was annoying. All of them are ignored now.

Bugfixes and updates older than May 2007

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