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ǃ ǃ tJD$T$4$ @u v @ u [^_]ÐU]Ít& ' UWVSO 4 軉}})t$1ED$E D$E$}9rރ [^_]Ë $ÐL$qZЁ RZ1U8 Mu}t 1߅t uMu}]aÍt& Ɓ u뺍 1 @ @E빐US^t^fЋu[]ÐUS [Ì3 Y[ Unknown Nexus Exception vector::_M_insert_aux Unknown nucleotide %c! Bad character state (%c) Error: Program terminated. (8HXhxCalling ActivateTaxon on uninitialized block gen mod topo brlen NNI randSPR limSPR
Calling InactivateTaxa on uninitialized block Calling IsActiveTaxon on uninitialized block Calling GetNumActiveTaxa on uninitialized block Calling GetNTaxTotal on uninitialized block Calling GetNTax on uninitialized block Calling InactivateTaxon on uninitialized block Calling ActivateTaxa on uninitialized block AppendNewLabel called on fixed label interface 0p P`@ 0p P`@ 30 p 0P`0 @ ,30 p@ P`0 H30 `@ 0P`0 3~P
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` P 0Zdp12SequenceData g3hE9MorphData g 3hE10BinaryData g83hE18NxsCharactersBlock gT3 3 30 21NxsTaxaBlockSurrogate f3g3 | 3, 21NxsCharactersBlockAPI f 423NxsLabelToIndicesMapper g(4@418NxsNCLAPIException gL4Pg12NxsException 4P @4@
g4 425NxsUnimplementedException 4` 3`
DpE`Eb0F`ePEOEEPa^U]V0~ PG@E3P 3`f514ErrorException f 6 N12NxsTaxaBlock16NxsX_NoSuchTaxonE ? ? |={Gz?{Gz\(\?\(\ =GARLI had a problem allocating memory! Try reducing the availablememory setting. ERROR: GamlConfig::General::Read(%s) failed.
Didn't find [general] section in config file
(this section heading is required) Either "megsclamemory" or "availablememory" must be specified in conf! Sorry, the collapsebranches option can not currently be used with checkpointing Didn't find [master] section in config file
(this section heading is required) Didn't find [remote] section in config file
(this section heading is required) Error: either "numberofprecreductions" (preferably) or "precreductionfactor" must be specified in conf! general logevery saveevery megsclamemory availablememory datafname ofprefix streefname constraintfile randseed refinestart outputeachbettertopology enforcetermconditions genthreshfortopoterm scorethreshforterm significanttopochange attachmentspertaxon outputmostlyuselessfiles outputphyliptree collapsebranches outputcurrentbesttopology outputcurrentbesttree restart writecheckpoints searchreps runmode ratehetmodel numratecats statefrequencies ratematrix invariantsites datatype geneticcode outgroup master remote nindivs holdover selectionintensity holdoverpenalty stopgen stoptime startoptprec minoptprec numberofprecreductions precreductionfactor topoweight modweight brlenweight randnniweight randsprweight limsprweight uniqueswapbias distanceswapbias treerejectionthreshold bootstrapreps resampleproportion inferinternalstateprobs gammashapebrlen gammashapemodel limsprrange intervallength intervalstostore meanbrlenmuts minbrlen maxbrlen startingbrlen random estimate 6rate gamma dna standard D HB @ zD pB B {Gz????333333?333333??:0yE>w [%s]
%s = %s
basic_string::erase true false could not open file "%s". basic_string::substr Error opening file "%s" for writing.
could not find string configuration entry "%s" configuration entry "%s" cannot be zero (possible problems reading this entry) configuration entry "%s" cannot be negative could not find float configuration entry "%s" error: could not find float configuration entry "%s" entry for option "%s" must be >=0 entry for option "%s" (%s) is greater than its max (%u) entry for option "%s" (%s) is not an integer could not find unsigned integer configuration entry "%s" could not find integer configuration entry "%s" entry for option "%s" must be >0 entry for option "%s" cannot be zero could not find boolean configuration entry "%s" expecting boolean (0 or 1) for entry "%s", found %s could not find integer range configuration entry "%s" could not find float range configuration entry "%s" A Atmpfile.txt %d %d qsstate.txt <-- top <-- i <-- bottom <-- j <-- x ,
%s : numbers %d and %d .comp Error saving data to file ' ': disk full? Sorry, taxon name %s for taxon #%d is too long (max length=%d) problem opening datafile %s for reading # of characters for taxon %s (%d) not equal
to the # of characters for first taxon (%d) problem reading data: name for taxon #%d too long Unexpected line break found while reading data for taxon %s Found extraneous information at end of phylip formatted datafile problem reading pattern counts #NEXUS
begin trees;
translate
(problem formatting some program output...) Error! Multiple sequences with same name encountered!: Terminating. Please make all sequence names unique! WARNING: The resampleproportion setting is the proportion to resample,
NOT the percentage (1.0 = 100%%).
The value you specified (%.2f) is a very large proportion. Resampling %d characters (%.2f%%).
Opening file "%s" for saving... Error: could not open file "%s" hE0 0" P`0 10DataMatrix fXEcould not open file: %s! #NEXUS brakmiss.log data file not found: %s! Attempting to read data file in Nexus format (using NCL): %s ... Problem reading nexus datafile Attempting to read data file in Fasta format: %s ... Attempting to read data file in Phylip format: %s ... A #B ;w?ŋ!r?{Gz? Q?{Gz?{Gz?{Gz?{Gz?{Gz?%s.restart%d.best.tre codon codon-aminoacid protein rna nucleotide invertmito empirical f1x4 f3x4 jones dayhoff wag mtmam mtrev poisson 2rate 1rate none nonsynonymous gammafixed flex Options: garli.conf -b --batch -i --interactive -v --version GARLI %s Version %.2f.%d zwickl@nescent.org -h --help %s.screen.log 13:11:47 Jul 4 2009 Compiled %s %s NCL version 2.1.00 Using %s
Reading config file %s
Summary of dataset: %d sequences. %d constant characters. %d autapomorphic characters. %d total characters. starting internal tests... ERROR.log
ERROR: %s
ratehetmodel set to "none", but numratecats is equal to %d! ratehetmodel set to "gamma", but numratecats is equal to 1! ratehetmodel set to "gammafixed", but numratecats is equal to 1! ratehetmodel set to "flex", but numratecats is equal to 1! ratehetmodel set to "nonsynonymous", but numratecats is equal to 1! 1 is the minimum value for numratecats. 20 is the maximum value for numratecats. Unknown setting for datatype: %s
(options are: codon, codon-aminoacid, aminoacid, dna, rna) Unknown genetic code: %s
(options are: standard, vertmito, invertmito) Sorry, ML estimation of equilibrium frequencies is not available under
codon models. Try statefrequencies = empirical
WARNING: to obtain good ML estimates of equilibrium aminoacid frequencies you
may need to run for a very long time or increase the modweight.
Consider statefrequencies = empirical instead.
Invalid setting for statefrequencies: %s
Options for all datatypes: equal, empirical, fixed
For all datatypes besides codon: estimate
For aminoacid datatype only: poisson, dayhoff, jones, wag, mtmam, mtrev
For codon datatype only: F1X4, F3X4 Sorry, %s is not a valid aminoacid rate matrix.
(Options are: dayhoff, jones, poisson, wag, mtmam, mtrev) Unknown setting for codon ratematrix: %s
(options are: 6rate, 2rate, 1rate, fixed) Unknown setting for dna/rna ratematrix: %s
(options are: 6rate, 2rate, 1rate, fixed) Invariant sites cannot be used with codon models.
Try ratehetmodel = nonsynonymous to allow dN/dS variation across sites Unknown setting for proportioninvariant: %s
(only valid option for codon models is none) invariant sites cannot be used with nonsynonymous rate variation Unknown setting for proportioninvariant: %s
(options are: none, fixed, estimate) Gamma rate heterogeneity cannot be used with codon models.
Try ratehetmodel = nonsynonymous to allow dN/dS variation across sites Unknown setting for ratehetmodel: %s
(options for codon datatype are: nonsynonymous, none) Invariant sites models should not be (and don't need to be) used
with the "flex" model of rate heterogeneity, since flex is able to
incorporate a class of sites with a rate of effectively zero Unknown setting for ratehetmodel: %s
(options are for nucleotide or aminoacid data are: gamma, gammafixed, flex, none) Usage: %s [OPTION] [config filename] -i, --interactive interactive mode (allow and/or expect user feedback) (interactive is the default for the version you are running) -b, --batch batch mode (do not expect user input) (batch is the default for the version you are running) -v, --version print version information and exit -h, --help print this help and exit -t run internal tests (requires dataset and config file) NOTE: If no config filename is passed on the command line the program
will look in the current directory for a file named "garli.conf" Copyright Derrick J. Zwickl 2005-2008 Unknown command line option %s Running serial GARLI, version 0.96beta8 (April 2008)
This version has undergone much testing, but is still a BETA VERSION.
- Please check results carefully! - using GNU gcc compiler version %d.%d.%d Error in config file...aborting %d parsimony-informative characters. %d characters were completely missing or ambiguous (removed). %d total characters (%d before removing empty columns). %d unique patterns in compressed data matrix.
******Successfully completed tests.****** the program must be compiled with ALLOW_SINGLE_SITE defined in defs.h to use site rate estimation (runmode = 8)!
-Press enter to close program.- not able to allocate enough memory!!! Q?Line: %ld Column: (y/n) Skipping unknown command ( block contains... Expecting ';' after block name, but found ENdblock ()[]{}/\,;:=*'"`-+<> Unexpected keyword ( end;
TAXA block found
TREES block found
ASSUMPTIONS block found
DISTANCES block found
CHARACTERS block found
DATA block found Reading block... CHARACTERS ASSUMPTIONS Opening GarliScore GarliModel ****NOTE (END OF NEXUS COMMENT) GarliReader> found dna data... found rna data... found protein data... found standard data... found nucleotide data... found continuous data... successful STOp STArt Replace Append File
Log file closed
Appending to log file
Replacing log file Ok to replace?
Log file opened
Log command aborted NCL encountered a problem reading the dataset. (press return to acknowledge) Must answer by typing either y or n and then pressing the Enter key Sorry, could not find specified file: %s Unexpected character(s) in Garli block.
See manual for model parameter format. Unexpected end of file encountered before "end;" or
"endblock;" command in Garli block ) encountered reading HELP command
Examples of use of available commands:
help -> shows this message
log file=mylog.txt start -> opens log file named mylog.txt
log stop -> closes current log file
exe mydata.nex -> executes nexus file mydata.nex
show -> reports on blocks currently stored
quit -> terminates application Expecting ';' to terminate the END or ENDBLOCK command, but found
Nexus blocks currently stored:
WARNING:Assumptions block found with multiple characters blocks.
Check output carefully to ensure that any excluded characters
were applied to the correct characters block.
The correct exclusion format in an Assumptions block is this:
EXSET * UNTITLED = 10-11;
But it will only be applied to the LAST characters block in the file.
You may want to comment out unused characters blocks.
Multiple GARLI blocks found (possibly in multiple files).
Remove or comment out all but one. Cannot issue execute command from within a GarliReader block Expecting ';' to terminate the EXECUTE command, but found Oops! Could not find specified file:
COMMENT FOUND IN NEXUS FILE (output verbatim): Error: the length of any one command cannot exceed Expecting an equals sign, but found ) encountered reading LOG command Cannot specify STOP with any of the following START, APPEND, REPLACE, FILE Cannot specify APPEND and REPLACE at the same time Cannot start log file since log file is already open Must provide a file name when opening a log file
e.g., log file=doofus.txt start replace; Log file specified already exists x`H0 dp
pEb`e EEPa^U]V0~ PG @ 0@ d` P| 0 p
p0
| cp
@
p12MyNexusToken gc@11GarliReader gc | , vector::reserve omega=%6.2f alpha=%6.2f flex rates=%6.2f pinv=%6.2f number of taxa added: Starting tree not compatible with constraint number %d!!! starting model/tree file "%s" does not exist! starting model/tree file "%s" could not be opened! Sorry, GARLI does not yet read Nexus tree files. See manual for starting tree/model format. Unknown model parameter specification! "%c" No starting tree or model was found in the specified starting conditions
file %s.
If it is a Nexus file it must start with #NEXUS
Otherwise see manual for information on starting condition format. Obtained starting tree %d from file %s No starting tree found in file %s Obtained starting or fixed model parameter values from file %s No starting model parameter values found in %s
Using default parameter values optimizing starting branch lengths and rate heterogeneity parameters... optimizing starting branch lengths and dN/dS (aka omega) parameters... optimizing starting branch lengths... pass %-2d: +%10.4f (branch=%7.2f scale=%6.2f
Optimizing parameters... improved %f lnL
Optimizing branchlengths... improved %f lnL 33333?@singular matrix in routine LUDecompose
Internal error in 'EigenRealGeneral'. rc = %d
@ > @? ffffff?-q r e f p
err IncompleteGamma CalcPmat CalcEigen proportion invariant alpha Rate props Rate mults Base frequencies Rate matrix pmat1 rate pmat2 rate o r %f %f %f %f %f e %f %f %f %f %f %f a %f p %f nst=1 nst=6 rmat=(%f %f %f %f %f) base=eq base=emp base=( %f %f %f) rates=gamma shape=%f ncat=%d rates=equal pinv=%f;
end;
pinv=%f [FLEX RATES: %f %f nst=2 trat=%f 6 rates 1 rate (ti/tv = %.4f) Amino Acid Rate Matrix: Jones Dayhoff Poisson WAG MtMam MtRev equal (1/60 = 0.01667, fixed) equal (1/62 = 0.01613, fixed) equal (1/61 = 0.01639, fixed) equal (0.05, fixed) equal (0.25, fixed) specified by user (fixed) estimated (ACGT) %.4f
Rate Heterogeneity Model: no rate heterogeneity %d dN/dS Proportion %5.4f %5.4f begin paup;
clear;
gett file= storebr;
lset userbr nst=6 rclass= nst=6 rmat=( base=( rates=gamma shape= ncat= pinv= ];
end;
nst=2 trat= Config file specifies ratematrix = 1rate, but starting model has nonequal rates!
Config file specifies ratematrix = 2rate, but starting model parameters do not match!
Provided relative rate parameters don't obey the ratematix specification!
Given this spec: %s, rates %d and %d should be equal.
Config file specifies equal statefrequencies,
but starting model has nonequal frequencies!
Config file specifies empirical statefrequencies,
but starting model contains frequencies!
Try statefrequencies = fixed or statefrequencies = estimate. Config file specifies "named" amino acid statefrequencies,
but starting model contains frequencies!
Try statefrequencies = fixed or statefrequencies = estimate. State frequencies do not appear to add up to 1.0!
Problem parsing rate matrix specification.
It should look something like this (a b a c b c) begin paup;
clear;
gett file=%s storebr;
lset userbr nst=6 rclass=%s rmat=(%f %f %f %f %f) ];
end;
[!THIS TREE INFERRED UNDER FLEX RATE MODEL WITH GARLI.
NO COMPARABLE MODEL IS AVAILABLE IN PAUP!]
WARNING: Omega parameter %d cannot be zero. Setting to 1e-5 omega category proportions add up to %f, not 1.0. Number of states = 60 (codon data, vertebrate mitochondrial code) Number of states = 62 (codon data, invertebrate mitochondrial code) Number of states = 61 (codon data, standard code) Number of states = 20 (amino acid data) Number of states = 4 (nucleotide data) One estimated dN/dS ratio (aka omega) = %f
Nucleotide Relative Rate Matrix Assumed by Codon Model: Nucleotide Relative Rate Matrix: User specified matrix type: %s values specified by user (fixed) AC = %.3f, AG = %.3f, AT = %.3f, CG = %.3f, CT = %.3f, GT = %.3f Equilibrium State Frequencies:
empirical values calculated by F3x4 method (fixed)
empirical values calculated by F1x4 method (fixed) empirical (observed) values (+F) empirical (observed) values, fixed: (AAA, AAC, AAG, AAT, ACA, ... etc)
(ACDEFGHIKLMNPQRSTVWY)
only an invariant (invariable) site category,
proportion specified by user (fixed)
%.4f only an invariant (invariable) site category, proportion estimated
%.4f nonsynonymous rate categories, rate and proportion of each estimated
(this is effectively the M3 model of PAML) discrete gamma distributed rate categories,
alpha param specified by user (fixed)
%.4f discrete gamma distributed rate categories, alpha param estimated
%.4f with an invariant (invariable) site category,
proportion specified by user (fixed)
%.4f with an invariant (invariable) site category, proportion estimated
%.4f Substitution rate categories under this model:
rate proportion FLEX rate categories, rate and proportion of each estimated with an invariant (invariable) site category,
proportion specified by user (fixed) with an invariant (invariable) site category, proportion estimated Estimated substitution rate categories:
rate proportion 2 rates (transition and transversion) K param = %.4f This dataset contains no constant characters!
Inference of the proportion of invariant sites is therefore meaningless.
Setting invariantsites to "none". [!THIS TREE INFERRED UNDER FLEX RATE MODEL WITH GARLI.
NO COMPARABLE MODEL IS AVAILABLE IN PAUP!] Rate matrix parameters can only be specified for nucleotide or codon models Problem reading rate matrix parameters from file.
Examine file and check manual for format.
Problem reading equilirium state frequency parameters from file.
Examine file and check manual for format.
Config file specifies ratehetmodel = flex, but starting model contains alpha!
Config file specifies ratehetmodel = nonsynonymous, but starting model contains alpha!
Problem reading alpha parameter from file.
Examine file and check manual for format.
Config file specifies ratehetmodel = none, but starting model contains alpha!
Problem reading proportion of invariant sites parameter from file.
Examine file and check manual for format.
Config file specifies invariantsites = none, but starting model contains it!
Flex rate parameters specified, but ratehetmodel is not flex!
Problem with flex rates specification in starting condition file Flex rate values specified in start file,
but ratehetmodel is not flex in conf file. WARNING: Flex rate multipliers cannot be zero. Rate %d changed from zero to 1.0e-5 Flex rate proportion %d cannot be zero. Specified Flex rate proportions don't add to 1.0!
Correct spec. is f rate1 prop1 rate2 prop2, etc. Omega parameters specified for non-codon model? Problem with omega parameter specification in starting condition file Problem with omega parameter specification in starting condition file
(wrong number of rate cats specified in config?) Unknown model parameter specification in file.
Examine file and check manual for format.
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ף*@9?q?@*?88c?:? ? @j@-q=+?-C 6?ư>IntDeriv TermDeriv ModDeriv Newton-Raphson rescale.log rescale reduced to too many passes in OptimizeBoundedParameter Problem with rescaling in branchlength optimization. Please report this error to zwickl@nescent.org.
Details: nd=%d init=%f cur=%f prev=%d iter=%d neg=%d Notice: possible problem with branchlength optimization.
If you see this message frequently, please report it to zwickl@nescent.org.
Details: nd=%d init=%f cur=%f prev=%d d1=%f d2=%f neg=%d Problem with branchlength optimization. Please report this error to zwickl@nescent.org.
Details: nd=%d init=%f cur=%f prev=%d d1=%f d2=%f neg=%d @ F ? H.?:h ?qh ?FN.?? @?{Gz3333@? @@Bootstrap rep (of Search rep modeldeb.log newindiv s= scr= fost= blenscr= subscr= allotscr #nexus begin trees; #nexus
begin paup;
set warnreset=no incr=auto;
execute .nex;
utree rates=gamma shape= pinv= nst=2 trat= );
);
lsc not enough memory parameter file not found bad dimensions specified undocumented error Quit? (y/n) --> Final Bootstrap rep %d (of %d) Search rep %d (of %d) %s.pop.check rb %s.adap.check %s.swaps.check tree final= [&U] [ ][ tree gen mut= subrec.log Subdef , subtrees, defined gen Last full recom gen gen
start with (node ) end tree bootrep ] begin trees;
translate
%d %s %s.phy .restart%d .rep%d %s%s%s.%s fate0%d.log problog0%d.log problem opening problog swaplog0%d.log gen uniqueSwaps totalSwaps
random seed = Restarting run at generation , seed , best lnL treelog0%d.tre MODEL REPORT: 6 rates empirical values (fixed) Replicate %d : %.4f (best) Replicate %d : %.4f (same topology as %d) .all.tre %s.all.phy tree rep BEST = [&U][!GarliScore ][!GarliModel swapped.tre Current score = %.4f Flex optimization: %f Omega optimization: %f pass %d %.4f Final score = %.4f stepwise Starting with seed=%d
Initial ln Likelihood: %.4f lnL after optimization: %.4f %s.siterates.log site# siteRate sitelnL NA NA final score: %f, %d sec
For this dataset: great >= %.0f MB continuing ... last_tree_imp precision current_lnL %-10s%-15s%-10s%-15s %-10d%-15.4f%-10.3f %-15d .current %-10d%-15.4f%-10.3f%-8d finished
>>>%s<<< >>>Completed %s<<<
>>>Terminated %s<<<
variable.log rep toporeport.log topo# ngen nInds inds ind topo root score orphans partscores.log attempt best root= if model mutation weight is set to zero,
statefrequencies cannot be set to estimate! if model mutation weight is set to zero,
invariantsites cannot be set to estimate! if model mutation weight is set to zero, ratematrix
must be fixed or 1rate! if model mutation weight is set to zero,
ratehetmodel must be set to gammafixed or none! Sorry, internal state reconstruction not yet implemented for non-nucleotide models.
PAML does a good job of this with fixed trees, so you might try using your best GARLI tree there. You cannont infer internal states during a bootstrap run! gett file=toscore.tre storebr; /scorefile=paupscores.txt replace;
/scorefile=paupscores.txt append;
problem reading swap checkpoint! Could not find checkpoint file %s!
Either the previous run was not writing checkpoints (checkpoint = 0),
the file was moved/deleted or the ofprefix setting
in the config file was changed. Problem reading checkpoint files. Scores of stored trees don't match calculated scores. Could not find checkpoint file %s!
Either the previous run was not writing checkpoints (checkpoint = 0),
the checkpoint files were moved/deleted or the ofprefix setting
in the config file was changed. nodenum size priority assigned brlen
taxa are in a subtree
remote localnode assignednode score
***NOTE: Run was terminated before termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!*** [!****NOTE: GARLI run was terminated before termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!***] [NOTE: GARLI Run was terminated before termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!]
[NOTE: GARLI Run was terminated before full completion! This is the best tree from a completed replicate.]
tree best = [&U][!GarliScore %f][!GarliModel tree bestREP%d = [&U][!GarliScore %f][!GarliModel [!****NOTE: GARLI Run was terminated before termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not be fully optimal!****] Restarting from checkpoint...
gen ind parent score MutType #brlen Time precision
gen best_like time optPrecision
One estimated dN/dS ratio (aka omega)
Nucleotide Relative Rate Matrix Assumed by Codon Model:
User specified matrix type: %s values specified by user (fixed) empirical values calculated by F3x4 method (fixed) empirical values calculated by F1x4 method (fixed) only an invariant (invariable) site category,
proportion specified by user (fixed) only an invariant (invariable) site category,
proportion estimated discrete gamma distributed rate cats,
alpha param specified by user (fixed) discrete gamma distributed rate cats, alpha param estimated 2 rates (transition and transversion)
Completed %d replicate runs (of %d).
Results: Final result of the best scoring rep (#%d) stored in %s.tre Final results of all reps stored in %s.all.tre [!****NOTE: The model parameters loaded are the final model estimates****
****from GARLI for the best scoring search replicate (# ).****
****The best model parameters for other trees may vary.****] Performing final branch optimization... Time used = %d hours, %d minutes and %d seconds Time used so far = %d hours, %d minutes and %d seconds Score after final optimization: Obtained starting tree %d from Nexus Problem getting tree(s) from NCL! Obtaining starting conditions from file %s Found model parameters specified in a Nexus GARLI block with the dataset,
and in the starting condition file (streefname).
Please use one or the other. Obtained starting or fixed model parameter values from Nexus: MODEL REPORT - Parameters are at their INITIAL values (not yet optimized) creating likelihood stepwise addition starting tree... creating likelihood stepwise addition starting tree (compatible with constraints)... creating random starting tree... creating random starting tree (compatible with constraints)... state frequencies specified as fixed, but no
Garli block found in %s!! alpha parameter specified as fixed, but no
Garli block found in %s!! proportion of invariant sites specified as fixed, but no
Garli block found in %s!! relative rate matrix specified as fixed, but no
Garli block found in %s!! state frequencies specified as fixed, but no
parameter values found in %s or %s! alpha parameter specified as fixed, but no
parameter values found in %s or %s! proportion of invariant sites specified as fixed, but no
parameter values found in %s or %s! relative rate matrix specified as fixed, but no
parameter values found in %s or %s! WARNING: Polytomies found in start tree. These were arbitrarily resolved. NOTE: Model contains no mutable parameters!
Setting model mutation weight to zero.
Making random trees compatible with constraints... Making stepwise trees compatible with constraints... Site-rate estimation complete. Sorry, Garli doesn't allow constraint trees in Nexus format.
See the manual for proper constraint format. Could not open constraint file %s! Loading constraints from file %s WARNING: You are running internal tests with NDEBUG defined!
It should not be defined for full error checking. bootstrap reweighting with seed %d No nexus trees block or Garli block was found in file %s,
which was specified
as source of starting trees No nexus trees block or Garli block was found in file %s,
which was specified
as source of starting model and/or tree Loading starting model and/or tree from file %s NOTE: Unlike many programs, the amount of system memory that Garli will
use can be controlled by the user. (This comes from the availablememory setting in the configuration file. Availablememory should NOT be set to more than the actual amount of physical memory that your computer has installed)
Memory to be used for conditional likelihood arrays specified as %.1f MB Mem level availablememory setting good approx %.0f MB to %.0f MB low approx %.0f MB to %.0f MB very low approx %.0f MB to %.0f MB the minimum required availablememory is %.0f MB
You specified that Garli should use at most %.1f MB of memory.
Garli will actually use approx. %.1f MB of memory **Your memory level is: great (you don't need to change anything)** **Your memory level is: good (you don't need to change anything)** **Your memory level is: low
(you may want to increase the availablememory setting)** **Your memory level is: very low
(if possible, you should increase the availablememory setting)** **NOT ENOUGH MEMORY
(you must increase the availablememory setting)** Not enough memory specified in config file (availablememory)! Perform final branch-length optimization and terminate now? (y/n) Reached termination condition!
last topological improvement at gen %d Reached termination condition!
Improvement over last %d gen = %.5f time limit of %d seconds reached... opt. precision reduced, optimizing branchlengths:%.4f -> %.4f
Restarting from checkpoint... The checkpoint loaded indicates that this run already completed.
To start a new run set restart to 0 and change the output
file prefix (ofprefix). rep number in checkpoint (%d) is larger than total rep specified in config (%d) %s generation %d, seed %d, best lnL %.3f MODEL REPORT - Parameter values are FINAL NOTE: ***Run was terminated before termination condition was reached!
Likelihood scores, topologies and model estimates obtained may not
be fully optimal!*** Saving best search rep (#%d) to bootstrap file Not saving search rep to bootstrap file due to early termination Inferring internal state probabilities on best tree.... >>>Internal state probabilities not inferred due to premature termination<<< Random seed for bootstrap reweighting: %d abandoning bootstrap rep %d ....terminating problem opening toporeport.log too many subtrees, increasing target size to paraMan->targetSubtreeSize... -C 6? ?333333?????{Gz?{Gzt?MbP? ? 8P I 5 V-?ffffff?MbP > ?GAMLN ARGUMENT IS LESS THAN OR EQUAL TO ZERO 9B.? * ?-|l @yD@;5/?@@Y2B@96SC@wz*E@r4dF@OOfq]@h b^@+NT_@ݭC#`@ ~{`@_bba@PSȐa@n b@0 Ib@)ca
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e@z9 Je@:GGʪ f@yuf@C g@g&g@oFh@·h@rQL i@ai@F~x*j@ P j@7k@+k@WFl@ l@tVm@eZNm@k9ihn@LQOUn@|a,~|o@j4nʼnp@'e Ip@gp@,Vp@/ q@4Gaq@q@>m#FJq@FK.5r@h)C|r@Trr@[]
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|y?{@?)Vy?POCG@d.Z@ P4@VB@} O@tXdj!cz|!#@Ћ} O@ llfSUUUUU?O I?㛢wC?$J?~lfPUUUU? A LCUnknown Amino Acid %c! vector::_M_range_check Excluded characters:
%10c%10c%10c%10c All bases were not observed at all codon positions!
You probably shouldn't be using F3x4 to estimate equilibrium codon frequencies.
Use F1x4 or equal state frequencies. State index out of range in NxsDiscreteDatatypeMapper::GetOneStateForCode Multiple characters/data blocks containing protein data found in Nexus datafile!
Either combine the blocks or comment one out. Ignoring non-protein characters block from Nexus datafile No characters/data blocks containing protein data found in Nexus datafile! Partially ambiguous characters of taxon %s converted to full ambiguity:
Multiple characters/data blocks containing nucleotide data found in Nexus datafile!
Either combine the blocks or comment one out. No characters/data blocks containing nucleotide data found in Nexus datafile! Ignoring non-nucleotide characters block from Nexus datafile Base usage at codon positions: pos 1 %10.5f%10.5f%10.5f%10.5f pos 2 %10.5f%10.5f%10.5f%10.5f pos 3 %10.5f%10.5f%10.5f%10.5f all pos %10.5f%10.5f%10.5f%10.5f
Codon to Aminoacid translation specified, but number of nucleotides not divisible by 3! Gaps or ambiguity codes found within codon for taxon %s.
Aminoacids coded as missing for that taxon: stop codon %s found at codon site %d (nuc site %d) in taxon %s. Bailing out. Codon datatype specified, but number of nucleotides not divisible by 3! Gaps or ambiguity codes found within codon for taxon %s.
Codons coded as missing for that taxon: WARNING: Not all allowable codons were observed in this dataset.
One pseudo-count will be added to each codon for caluclation of the
empirical frequencies. You should probably use
statefrequencies = f1x4 or f3x4 instead of empirical.
Model specified as aminoacid, but nucleotide data found! WARNING: Not all amino acids were observed in this dataset.
One pseudo-count will be added to each amino acid for calculation of the
empirical frequencies. You should probably use
a statefrequencies setting other than emprical.
r r r r r r r r r r r r r r r r r r r к r p ` P @ r 0 r й r r r r r r r r r к r p ` P @ r 0 r й r ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' ' P л ' ' 0 ' ' @ ' ' ' ' x x ' ' ' ' ' ' ' ' P л ' ' 0 ' ' @ ' ' ' ' x x ' (0 ` p 0P` 0 @ 0 0 p 0P` 0 P @ 0 ` ` p 0P`0 0 @ @13AminoacidData g39CodonData g314NucleotideData g3 @@translate ; 0 1 2 ClaIntInt ClaIntTerm ClaTermTerm Rescale ScoreInt ScoreTerm EQVectors biparts.log claind.log root tots starting score:%f determImpsDistR.%d.%f.tre determImpsDist.%d.%f.tre determDistR%d.%f.log determDist%d.%f.log %f %f %d %d = [&U][ %d %d %f
dist = %d done. %d swaps, %d accepted determImpsCutR.%d.%f.tre determImpsCut.%d.%f.tre determCutR%d.%f.log determCut%d.%f.log determImpsRand.%d.%f.tre determRand%d.%f.log %d swaps before reset %d swaps before completion %s.internalstates.log | Bipartition %d: %s Number of taxa from checkpoint (%d) is not the same as in the current
datafile (%d)! The checkpoint seems to be from a different run! nonunique swap > NNI found! %d %d %d Problem with rescaling during tree scoring. Please report this error to zwickl@nescent.org. Entirely uninformative character (gaps,N's or ?'s)
Problem reading tree description. Mismatched parentheses? ->Branch of length %s is less than min of %.1e. Setting to min. ->Branch of length %f is greater than max of %.0f. Setting to max. Warning: extraneous character (%c) found after ; in tree description Unexpected character found in tree description at this point: %s Unexpected character(s) found in tree description "%s!" Taxon number in tree description (%d) is greater than
number of taxa in dataset! Unknown taxon "%s" encountered in tree description! Problem parsing tree string! Expecting : or , or ), found %c Number of taxa in tree description (%d) not equal to number of taxa in dataset (%d)! constraint string must start with '+' (positive constraint) or '-' (negative constraint) constraint # %d does not have the correct number of characters!
(has %d) constraint strings must start with
'+' (positive constraint) or '-' (negative constraint)
followed by either a ...*** type specification
or a constraint in newick format.
Note that backbone constraints cannot be specified in ...*** format. Constraint represents a fully resolved tree!
If you would like to fix the tree topology during a run,
do so by specifying your tree as a starting tree and
setting topoweight to 0.0 Specified constraint does not constrain any relationships.
See manual for constraint format Sorry, GARLI can currently only handle a single negatively (conversely) constrainted branch (bipartition):-( problem with constraint # %d
constraint strings must start with
'+' (positive constraint) or '-' (negative constraint)
followed by either a ...*** type specification
or a constraint in newick format cannot mix positive and negative constraints! Sorry, GARLI can currently only handle a single negatively (conversely) constrainted branch :-( Found %d positively constrained bipartition(s) Bipartition %d (backbone): %s Found 1 negatively (conversely) constrained bipartition constraints are not compatible with one another! HC Zd;O?u?j/ ףp=
?в9?]tE?Gz?bph>?@x D%.8lf %.10lf Input tree has polytomies!! WTF? There appears to be a problem with a tree specification string.
Check for extra parentheses. 1 character set defined: character sets defined: No taxon sets were defined 1 taxon set defined: taxon sets defined: 1 exclusion set defined: exclusion sets defined: (default) taxa != __null tb != __null The symbol was not recognized * = WtSet ' : LINK CHARACTERS = TREES = OPTIONS DefType = GapMode = NewState PolyTCount = MinSteps PolyTCount = MaxSteps vector::_M_fill_insert UserType (Stepmatrix) = . " instead. charBlockPtr != __null UNIVERSAL UNIVERSAL.EXT MTDNA.DROS MTDNA.DROS.EXT MTDNA.MAM MTDNA.MAM.EXT MTDNA.YEAST Type name not found. Unknown TAXA block ( Unknown CHARACTERS block ( Unknown TREES block ( is a not a valid . Only entries for An * is ignored in a BEGIN SETS;
TAXSET CHARSET TREESET TaxPartition CharPartition TreePartition END;
BEGIN CODONS;
CodonPosSet CodeSet BEGIN ASSUMPTIONS;
EXSET TypeSet CharSet Character A CHARSET with the name SETS CODONS treesBlockPtr != __null TreeSet Trees A TreeSet with the name TaxSet Taxon A TaxSet with the name ExSet A ExSet with the name ) in the definition of , token.Equals(",") . At least one ) is not included UNORD IRREV IRREV.UP IRREV.DOWN DOLLO DOLLO.UP DOLLO.DOWN STRAT SQUARED LINEAR A TREES block with the title must precede an block with a VECTOR STANDARD in TreeSet definition NOTOKENS in TreePartition definition treesBlockPtr Tree A TAXA block in TAXSET definition in TaxPartition definition Taxa A CHARACTERS (or DATA) block DEFTYPE effAssumpB cb POLYTCOUNT MINSTEPS MAXSTEPS Unknown value ( GAPMODE NEWSTATE Skipping unknown subcommand ( ) in OPTIONS command of Block after "(Characters" in a ; encountered in Skipping unknown as a qualifier is not supported. qualifier: The cbp UNALIGNED The Genetic code name effectiveAssumpBlock The group name CSTREE REALMATRIX STEPMATRIX UserType qualifier in UserType definition UserType in UserType stepmatrix. - INF Unrecognized state WtSet Invalid weight found in a WtSet command. BEGIN CHARPARTITION CODESET CODONPOSSET TAXPARTITION TREEPARTITION TYPESET USERTYPE WTSET block contains the following: No character sets were defined No exclusion sets were defined ../.././ncl/nxsassumptionsblock.cpp Expecting a number as a character weight. Found " Resetting a used charLinkStatus Resetting a used taxaLinkStatus Standard (predefined) types cannot be fetched using GetIntType. is not the name of a known type (and therefore is not a valid default type) No NxsReader when reading Assumptions block. LINK to a Taxa block must occur before commands that use a taxa block ) referred to in the LINK command LINK to a CHARACTERS block must occur before commands that use a CHARACTERS block LINK to a TREES block must occur before commands that use a TREES block Skipping unknown LINK subcommand: (s) were included in the definition has already been encountered. The later definition will preempt the earlier definition(s). An * is ignored in a CHARSET command An * is ignored in a TreeSet command An * is ignored in a TaxSet command Illegal repitition of a subset name ( Expecting a : after the subset name is a predefined type which cannot be redefined
(If such a block exists, then this program may not be using an API for the NCL library that supports block linking). Multiple TREES blocks have been encountered, but a command was found which does not specify which TREES block it uses. The most recent TREES block will be used. after "(Trees" in a TreeSet command VECTOR-style set definitions are not currently supported ; encountered in TreeSet command before parentheses were closed Skipping unknown TreeSet qualifier: after "(Trees" in a TreePartition command NOTOKENS-style set definitions are not currently supported ; encountered in TreePartition command before parentheses were closed Skipping unknown TreePartition qualifier: Multiple TAXA blocks have been encountered, but a command was found which does not specify which TAXA block it uses. The most recent TAXA block will be used. after "(Taxa" in a TaxSet command ; encountered in TaxSet command before parentheses were closed Skipping unknown TaxSet qualifier: after "(Taxa" in a TaxPartition command ; encountered in TaxPartition command before parentheses were closed Skipping unknown TaxPartition qualifier: Multiple CHARACTERS blocks have been encountered, but a command was found which does not specify which CHARACTERS block it uses. The most recent CHARACTERS block will be used. is not a valid type name for OPTIONS DefType. Expceting one of:
) found for OPTIONS PolyTCount (expecting MINSTEPS or MAXSTEPS). ) found for OPTIONS GapMode (expecting MISSING or NEWSTATE). The Codon Position category name found in a CodonPosSet command is not legal. "N", "1", "2", or "3" were expected. found in a CodeSet command does not correspond to a known code found in a TypeSet command does not correspond to a known type An * is ignored in a UserType command after "(Characters" in a UserType command NOTOKENS-style UserType are not supported ; encountered in UserType command before parentheses were closed Skipping unknown UserType qualifier: should occur in parentheses ( Tree description queries are only supported on processed tree descriptions. No datatype was found with all of the symbols the UserType CSTree Expecting a number of states after the = in the UserType command (the number of states must be greater than one). Found ; prematurely terminated the state declaration portion of a UserType stepmatrix. State names cannot be repeated in a UserType stepmatrix. was encountered more than once. Expecting a number or i (for infinity) as an element of the UserType stepmatrix. Found Expecting ; at the end of the UserType command. Found h0 p D `Eb0F@e*EPaPU V0~0A PGP@0Pp` аp 126NxsAssumptionsBlockFactory gH19NxsAssumptionsBlock gtfg| 15NxsBlockFactory 22NxsAssumptionsBlockAPI p virtual unsigned int NxsAssumptionsBlock::TaxonLabelToNumber(NxsString) const void NxsAssumptionsBlock::HandleOptions(NxsToken&) virtual void NxsAssumptionsBlock::ReadTreesetDef(NxsString, NxsToken&, bool) virtual void NxsAssumptionsBlock::ReadTaxsetDef(NxsString, NxsToken&, bool) void NxsBlock::ReadPartitionDef(NxsPartition&, NxsLabelToIndicesMapper&, const std::string&, const char*, const char*, NxsToken&, bool, bool, bool) void NxsAssumptionsBlock::HandleTreePartition(NxsToken&) void NxsAssumptionsBlock::HandleTaxPartition(NxsToken&) virtual void NxsAssumptionsBlock::ReadExsetDef(NxsString, NxsToken&, bool) virtual void NxsAssumptionsBlock::ReadCharsetDef(NxsString, NxsToken&, bool) void NxsAssumptionsBlock::HandleCharPartition(NxsToken&) void NxsAssumptionsBlock::HandleWeightSet(NxsToken&) void NxsAssumptionsBlock::HandleCodonPosSet(NxsToken&) void NxsAssumptionsBlock::HandleCodeSet(NxsToken&) void NxsAssumptionsBlock::HandleUserType(NxsToken&) void NxsAssumptionsBlock::HandleTypeSet(NxsToken&) void NxsAssumptionsBlock::ApplyExset(NxsString) void NxsAssumptionsBlock::ReplaceTaxaBlockPtr(NxsTaxaBlockAPI*) Tp0 g`|24WtSetVectorItemValidator f25NxsSetVectorItemValidator |`P p 0@P g316BogusToIndMapper `0
DpE`Eb0F`ePEOEEPa^U]V0~ PG@E END or ENDBLOCK TITLE END Unexpected token . Expecting , but found: BLOCKID TITLE Expecting '=' but found ; instead Expecting a number or label, found Expecting a ). Found NxsBlock::WriteLinkCommand NxsBlock::WriteAsNexus NxsBlock::HandleLinkCommand CloneBlock an id for the block BLOCKID a title for the block " will be replaced by " Skipping command: name or a number corresponding to a 's number (a number from 1 to Multiple TITLE commands were encountered the title " | RP
DpE`Eb0F`ePEOEEPa^U]V0~ PG@E8NxsBlock fp RNA DNA Nucleotide Protein Continuous ACGT ACGU ACDEFGHIKLMNPQRSTVWY* 01 vector::_M_insert_aux Expecting a DNA base yeastmito moldmito ciliate echinomito euplotid plantplastid altyeast ascidianmito altflatwormmito blepharismamacro chlorophyceanmito trematodemito scenedesmusmito thraustochytriummito ELIMINATE firstPos == 0L secondPos == 0L thirdPos == 0L block contains no taxa one taxon and no characters one character Data type is " Respecting case Ignoring case Missing data symbol is ' Match character is ' No gap character specified Valid symbols are: Equate macros in effect: no characters excluded Data matrix: VertMito YeastMito MoldMito InvertMito Ciliate EchinoMito Euplotid PlantPlastid AltYeast AscidianMito AltFlatwormMito BlepharismaMacro ChlorophyceanMito Trematodemito ScenedesmusMito ThraustochytriumMito Unrecognized genetic code. Expecting a triplet of bases Error reading character (name " Eliminate eliminated.size() <= nChar of taxon number {AG} {AC} {CG} {ACG} {CT} {GT} {AT} {ACT} {CGT} {AGT} {ACGT} {CU} {GU} {AU} {ACU} {CGU} {AGU} {ACGU} {DN} {EQ} {ACDEFGHIKLMNPQRSTVWY*} { of taxon " Invalid state specified " a number values read. stateCodeLookupPtr stateAsNexus.length() > 0 !tokens charNum < row.size() ssi == &stateSetInfo mapper != __null endCharInd <= this->nChar endCharInd <= row.size() endCharInd <= rs Writing character state mapper missing != '\0' nStates > 0 NXS_MISSING_CODE == stateCode convertToStandard states ( no gaps including the gap "state" state codes.
CHARLABELS _ CharStateLabels
,
/ Matrix
TrematodeMito Invalid character number ( / " instead FORMAT Datatype= Missing= Gap= Symbols=" Equate=" FORMAT Datatype=MIXED( RespectCase MatchChar= Items = ( StatesFormat=StatesPresent StatesFormat=Individuals Tokens Interleave BEGIN CHARACTERS;
DIMENSIONS NTax= NChar= in DIMENSIONS command Dimensions
A NCHAR NEWTAXA CHARSTATELABELS Data for this character ( ) has already been saved States for character have already been stored was unexpected. Data for this character POS1 POS2 POS3 NONCODING CONSTANT GAPPED STATES taxa in the Matrix command. Data for this taxon ( Unexpected ; (after only characters were read) Could not find taxon named " " among stored taxon labels Characters for taxon " " (number and " " was not expected. ) have already been saved currMapper ;[
" but found *sIt < 0 0123456789 Matrix Must precede after keyword DATATYPE NUCLEOTIDE PROTEIN RESTRICTION CONTINUOUS AVERAGE MIXED mixed datatype definition Datatype=Mixed RESPECTCASE after keyword MISSING was specified was specified) after keyword GAP after keyword MATCHCHAR SYMBOL after keyword SYMBOLS " to start the symbols list was found closing " of symbols list SYMBOLS defines new states but only The character Adding symbols to the MIXED datatype matrix STANDARD datatype matrix datatype. after keyword EQUATE EQUATE symbol specified ( NOLABELS TRANSPOSE after keyword ITEMS after keyword STATESFORMAT STATESPRESENT INDIVIDUALS The "missing" character ' The "matchchar" character ' The "gap" character ' in EQUATE definition nucIt != endNucIt vector::_M_range_check AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATC ATG ATT CAA CAC CAG CAT CCA CCC CCG CCT CGA CGC CGG CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT TTA TTC TTG TTT ppp qqqpp2qqqxqqPq}}wmcYwOrr"vvvv"vuvvwwwxwwhwҢu bool NxsCharactersBlock::IsPolymorphic(unsigned int, unsigned int) const std::set, std::allocator >& NxsDiscreteDatatypeMapper::GetStateSetForCode(int) const unsigned int NxsCharactersBlock::GetNumStates(unsigned int, unsigned int) void NxsCharactersBlock::ShowStateLabels(std::ostream&, unsigned int, unsigned int, unsigned int) const virtual void NxsCharactersBlock::HandleTransposedMatrix(NxsToken&) virtual void NxsCharactersBlock::HandleStdMatrix(NxsToken&) void NxsCharactersBlock::HandleEliminate(NxsToken&) void NxsCharactersBlock::WriteStatesForTaxonAsNexus(std::ostream&, unsigned int, unsigned int, unsigned int) const int NxsDiscreteDatatypeMapper::StateCodeForNexusMultiStateSet(char, const std::string&, NxsToken&, unsigned int, unsigned int, const NxsDiscreteStateRow*, const NxsString&) int NxsDiscreteDatatypeMapper::StateCodeForNexusPossibleMultiStateSet(char, const std::string&, NxsToken&, unsigned int, unsigned int, const NxsDiscreteStateRow*, const NxsString&) bool NxsCharactersBlock::HandleNextDiscreteState(NxsToken&, unsigned int, unsigned int, NxsDiscreteStateRow&, NxsDiscreteDatatypeMapper&, const NxsDiscreteStateRow*, const NxsString&) void NxsDiscreteDatatypeMapper::WriteStateCodeAsNexusString(std::ostream&, int, bool) const bool NxsDiscreteDatatypeMapper::IsPolymorphic(int) const int NxsDiscreteDatatypeMapper::StateCodeForStateSet(const std::set, std::allocator >&, bool, bool, char) void NxsDiscreteDatatypeMapper::RefreshMappings(NxsToken*) bool NxsCharactersBlock::AugmentedSymbolsToMixed() void NxsCharactersBlock::CreateDatatypeMapperObjects(const NxsPartition&, const std::vector >&) static NxsCharactersBlock* NxsCharactersBlock::NewCodonsCharactersBlock(const NxsCharactersBlock*, bool, bool, bool, const std::list >*, NxsCharactersBlock**)
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! " # $ % & ' ( ) * + , - . / 0 1 2 3 4 5 6 7 8 9 : ; < Unrecognized genetic code name: ../.././ncl/nxscharactersblock.cpp Expecting partition subsets named 1, 2, and 3 Expecting the partition subsets named 1, 2, and 3 to have the same size Multicharacter tokens allowed in data matrix Data matrix entries are expected to be single symbols Character labels are expected on left side of matrix Taxon labels are expected on left side of matrix No labels are expected on left side of matrix Character and character state labels: (no label provided for this character) Matrix transposed and interleaved Matrix transposed but not interleaved Matrix interleaved but not transposed Matrix neither transposed nor interleaved No match character specified Gap character specified is ' No equate macros have been defined No characters were eliminated The following characters were eliminated: The following characters have been excluded:
Unrecognized genetic code enumeration: Only one ELIMINATE command should be used in a CHARACTERS or DATA block (it must appear before the MATRIX command).
New character eliminations will be added to the previous eliminated characters (the previously eliminated characters will continue to be excluded). found while reading character Character index is ExcludeCharacter out-of-range. Must be < Number of character labels exceeds NCHAR specified in DIMENSIONS command Unexpected empty token encountered Currently polymorphism and ambiguity are not supported for matrices in TOKENS mode: Unexpected use of MatchChar in first taxon with data. MatchChar found for character number but the first taxon does not have a character state stored for this character. For each cell of the MATRIX a value for each of the ITEMS listed in the FORMAT command is expected.
Only Internal Error: character index out of range in continuousMatrix. MATCHCHAR cannot be used in the first taxon First taxon does not have a value to copy, but a MATCHCHAR was found. Illegal usage of NXS_GAP_STATE_CODE in a datatype without gaps Illegal usage of NXS_INVALID_STATE_CODE as a state index Illegal usage of unknown negative state index Illegal usage of state index >= the number of states Expecting a state symbol of set of symbols in () or {} braces. Found (poly && *endIt == ')') || (!poly && *endIt == '}') A state range cannot start with is not a valid state range (the end state is a lower index than the start) State range not terminated -- ending in ~ An illegal (empty) state range was found " A state range cannot end with Expecting {} or () around a multiple character state set. Found Illegal usage of NXS_INVALID_STATE_CODE as a state code Illegal usage of state code > the highest state code ../.././ncl/nxscharactersblock.h No symbol found for state code Char buffer too small in NxsCharactersBlock::WriteStates No DatatypeMapper in WriteStatesForTaxonAsNexus No DatatypeMapper for character in WriteStatesForTaxonAsNexus , but no appropriate chararcter label or symbol was found. Taxon index out of range of NxsCharactersBlock::IsPolymorphic Character index out of range of NxsCharactersBlock::IsPolymorphic Cannot create a datatype mapper with no symbols Cannot create a datatype mapper with no missing data symbol cLookup[(int) missing] == NXS_MISSING_CODE Cannot create a mixed datatype mapper NEXUS State Code States
KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF KNKNTTTT*S*SMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF KNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVQYQYSSSS*CWCLFLF NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSCCWCLFLF KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLSLEDEDAAAAGGGGVVVV*Y*YSSSS*CWCLFLF KNKNTTTTGSGSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF NNKNTTTTSSSSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVVYY*YSSSSWCWCLFLF KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YQYSSSS*CWCLFLF KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YLYSSSS*CWCLFLF NNKNTTTTSSSSMIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSSWCWCLFLF KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*YLY*SSS*CWCLFLF KNKNTTTTRSRSIIMIQHQHPPPPRRRRLLLLEDEDAAAAGGGGVVVV*Y*YSSSS*CWC*FLF No DatatypeMapper in GetNamedStateSetOfColumn No DatatypeMapper in FindConstantCharacters DeleteStateIndices can only delete fundamental states DeleteStateIndices can not currently work on datatypes with equates Invalid characters block (no datatype mapper) Characters block must be of the type codons when RemoveStopCodons is called Characters block must be an uncompressed codons type when RemoveStopCodons is called Stop codon found at character STATELABELS cannot be specified when the datatype is continuous ) found in STATELABELS command (either out of range or not interpretable as an integer) ) found in CHARSTATELABELS command (either out of range or not interpretable as an integer) Expecting a comma or semicolon here, but found " State Labels cannot be specified when the datatype is continuous after NTAX in DIMENSIONS command DIMENSIONS command must have an NCHAR subcommand . DIMENSIONS command must have an NTAX subcommand when the NEWTAXA option is in effect. A TAXA block must be read before character data, or the DIMENSIONS command must use the NEWTAXA. block must be less than or equal to NTAX in TAXA block
Note: one circumstance that can cause this error is
forgetting to specify in DIMENSIONS command when
a TAXA block has not been provided block must contain a Matrix command Could not find character named among stored character labels The order of characters must be in the same order in each page of the interleaved matrix. Character Each line within an interleave page must comprise the same number of taxa Each line within an interleave page must comprise the same number of taxa
. Expecting the end of a line, but found Not enough taxlabels are known to read characters for
Expecting data for taxon " indOfTaxInMemory < continuousMatrix.size() indOfTaxInMemory < discreteMatrix.size() " according to the taxa block) have already been stored Ordering of taxa must be identical to that in first interleave page. Taxon " Each line within an interleave page must comprise the same number of characters. Error reading taxon " Each line within an interleave page must comprise the same number of characters
. Expecting the end of a line, but found when reading data for taxon " Expecting a whitespace character at the end of the characters for taxon " dtParts.size() == dtcodes.size() block with a TAXA block or specify NEWTAXA and NTAX in the DIMENSIONS command Reading of transposed, mixed datatype matrices will probably never be supported by NCL after "DATATYPE =" in FORMAT command after "DATATYPE=MIXED" in FORMAT command. Expecting ( Expecting ( after "DATATYPE=MIXED" but found after "DATATYPE=MIXED(" in FORMAT command. Expecting a datatype in "DATATYPE=MIXED" in FORMAT command. Expecting a closing ) to terminate the list. Error parsing "DATATYPE=MIXED" subcommand in FORMAT the command. is not a valid DATATYPE within a after DATATYPE in FORMAT command after DATATYPE = in FORMAT command Only one FORMAT command should occur per DATA or CHARACTERS block. after "MISSING = " in FORMAT command MISSING symbol should be a single character, but MISSING symbol specified cannot be a punctuation token ( MISSING symbol specified cannot be a whitespace character ( after "GAP = " in FORMAT command GAP symbol should be a single character, but GAP symbol specified cannot be a punctuation token GAP symbol specified cannot be a whitespace character after "MATCHCHAR = " in FORMAT command MATCHCHAR symbol should be a single character, but MATCHCHAR symbol specified cannot be a punctuation token ( MATCHCHAR symbol specified cannot be a whitespace character ( SYMBOLS subcommand not allowed for DATATYPE=CONTINUOUS SYMBOLS subcommand not allowed for DATATYPE=RESTRICTION Expecting " after Symbols= but new states allowed for this DATATYPE A ~ in a SYMBOLS list is interpreted as a range of symbols. The ~ cannot be the first or last character in the symbols list Endpoint of SYMBOLS range must be greater than the starting point. This was not true of is an illegal SYMBOLS range. A range must go from a letter to a letter or from a number to number defined in SYMBOLS is predefined for this DATATYPE and should not occur in a SYMBOLS statement defined in SYMBOLS subcommand, has already been introduced as an EQUATE key. The use of a character as both a state symbol and an equate key is not allowed. datatype will cause the matrix to be treated as if it were a Symbols cannot be added to the EQUATE subcommand not allowed for DATATYPE=CONTINUOUS " to start the Equate definition Expecting '"' after keyword EQUATE but found " to end the Equate definition Expecting single-character EQUATE symbol but found ) is not valid. Equate symbols cannot be any of the following: ()[]{}/\,;:=*'"`<>^ ) is not valid; An Equate symbol cannot be a state symbol or identical to the missing, gap, or matchchar symbols. State or set of states in Equate definition } to close the state set in an equate definition ) to close the state set in an equate definition after "ITEMS =" in FORMAT command ) to close Items list in FORMAT command Sorry, only ITEMS=STATES is supported for discrete datatypes at this time after "STATESFORMAT =" in FORMAT command Sorry, only STATESFORMAT=STATESPRESENT or STATESFORMAT=INDIVIDUALS are supported for continuous datatypes at this time Sorry, only STATESFORMAT=STATESPRESENT supported for discrete datatypes at this time NOTOKENS is not allowed for the CONTINUOUS datatype ' may not be included in the SYMBOLS list. MatchChar and Gap symbol cannot be identical! Both were set to MatchChar and Missing symbol cannot be identical! Both were set to Gap symbol and Missing symbol cannot be identical! Both were set to TOKENS must be defined for DATATYPE=CONTINUOUS TOKENS not allowed for the DATATYPEs DNA, RNA, or NUCLEOTIDE The combination of DATATYPE=Mixed and TOKENS are not currently supported. Cannot create a codons block with a number of characters that is not a multiple of 3 NewCodonsCharactersBlock is not implemented for cases in which you are not mapping any ambiguity to the missing state code. NewProteinCharactersBlock is not implemented for cases in which you are not mapping any ambiguity to the missing state code. NewProteinCharactersBlock must be called with a block of codon datatype Pnn25NxsCharactersBlockFactory g4DATA ##" P('P
`Eb0Fe |!EPa`zUV0~p( PG@ P@"p0@ 51 oo60PвP@@('o6p
` P 0('Zdp19NxsDataBlockFactory g12NxsDataBlock g3 FORMAT Missing = Triangle = Lower Diagonal;
0.0 BEGIN DISTANCES;
DIMENSIONS NChar = Matrix is lower-triangular Matrix is upper-triangular Matrix is rectangular Matrix is interleaved Matrix is non-interleaved Taxon labels provided No taxon labels provided Diagonal elements specified Missing data symbol is NTAX in after TRIANGLE LOWER UPPER BOTH NODIAGONAL NOINTERLEAVE after MISSING Token specified ( Taxon Taxon labeled Could not find BEGIN DISTANCES Diagonal elements not specified block must be less than or equal to NTAX in TAXA block
Note: one circumstance that can cause this error is
forgetting to specify NTAX in DIMENSIONS command when
a TAXA block has not been provided Expecting UPPER, LOWER, or BOTH but found Missing data symbol specified ( ) is invalid (must be a single character) ) is an invalid subcommand for the FORMAT command was not expected in the DISTANCES matrix.
Taxa should be in the same order as in the Taxon block was encountered more than one time in the Distances Matrix. is out of order compared to previous interleave pages among taxa previously defined Too many distances specified in row just read in Illegal internal row number for taxon in Distance Matrix. MATRIX command cannot be read if NTAX is zero Cannot specify NODIAGONAL and TRIANGLE=BOTH at the same time ee/ @,1Pe
DpE`Eb0Fee7*PhEPa7UeV0~l PG0h@bepep
` P 0,1Zdp24NxsDistancesBlockFactory gx17NxsDistancesBlock g | 3, [!Skipping disabled block ( )...] [!Skipping unknown block ( ../.././ncl/nxsreader.cpp curr != __null newBlock != __null
Warning: at line , column (approximately) (file position )
, column ):
WARNING:
oldBlock != __null Could not open the file " Untitled Block %u has already been used for a nb storing implied block: storing read block: Unexpected End of file in &SHOWALL &LEAVE BEGIN Copyright (c) 1999-2003 by Paul O. Lewis http://sourceforge.net/projects/ncl Expecting ';' after END or ENDBLOCK command, but found " does not refer to a valid file. mIt != blockTitleHistoryMap.end() Block titles cannot be repeated. The TITLE Expecting #NEXUS to be the first token in the file, but found P P|}}`|p|}}p~
| P|}}`|p|}
}}}
|25ExceptionRaisingNxsReader gx9NxsReader f void NxsReader::AddBlockToUsedBlockList(const std::string&, NxsBlock*, NxsToken*) void NxsReader::NewBlockTitleCheckHook(const std::string&, NxsBlock*, NxsToken*) void NxsReader::BlockReadHook(const NxsString&, NxsBlock*, NxsToken*) void NxsReader::Detach(NxsBlock*) void NxsReader::Reassign(NxsBlock*, NxsBlock*) virtual void NxsReader::Add(NxsBlock*) g@418NxsX_UnexpectedEOF P \ Error in the descriptor of a command.
. Encountered ../.././ncl/nxssetreader.cpp last >= first last !=(2147483647 * 2U + 1U) ) in multiple subsets. Set element ( ) not a number and not a valid taxon label \ The modulus value label in the Range in the set definition in the End of a range in a - command. Encountered descriptor (number or label) in the stride !=(2147483647 * 2U + 1U) Illegal repitition of an index ( and not a valid character label The symbol '-' is out of place here The symbol '.' can only be used to specify the end of a range The symbol '\' can only be used after the end of a range has been specified Character number out of range (or range incorrectly specified) in set specification Number out of range (or range incorrectly specified) in set specification The '-' must be preceded by number or a command must be closed with a number or label. command must be closed with a single number or label (not a set). command must be a larger index than the start of the range (found Expecting a positive number indicating the 'stride' after the \ in the static void NxsSetReader::AddRangeToSet(unsigned int, unsigned int, unsigned int, NxsUnsignedSet*, const NxsUnsignedSet*, NxsToken&) fN9NxsString15NxsX_NotANumberE '[_ 0123456789-.+ 0123456789-+ %#3.6f basic_string::at ../.././ncl/nxsstring.cpp n > 3 %%.%df w >= tmp.length() w >= s.length() x_width <= num_spaces %lu NxsString& NxsString::ShortenTo(unsigned int) NxsString& NxsString::RightJustifyString(const NxsString&, unsigned int, bool) NxsString& NxsString::RightJustifyDbl(double, unsigned int, unsigned int, bool) NxsString& NxsString::RightJustifyLong(long int, unsigned int, bool) BEGIN TAXA;
DIMENSIONS NTax = 1 taxon TAXLABELS The taxon index is out of range. Only taxa in block. has already been stored. Illegal TaxLabel found:
BEGIN TAXA after NTAX LINK TAXA = The label for taxon Taxon index out of range in InactivateTaxon NEWTAXA must have been specified in DIMENSIONS command to use the TAXLABELS command in a Number of stored labels exceeds the NTax specified. TaxLabels cannot be repeated. The label
TaxLabels cannot be punctuation. Expecting NTAX keyword, but found API Error: No nxsReader during parse in NxsTaxaBlockSurrogate::HandleLinkTaxaCommand API Error: No nxsReader during parse in NxsTaxaBlockSurrogate::AssureTaxaBlock TAXA Block has been not been read, but a command (which requires a TAXA block) has been encountered. Either add a TAXA block or (for blocks other than the TREES block) you may use a "DIMENSIONS NEWTAXA NTAX= ..." command to introduces taxa. Multiple TAXA Blocks have been read (or implied using NEWTAXA in other blocks) and a command (which requires a TAXA block) has been encountered.
A "LINK TAXA=;" command must be used to specify which TAXA block is needed. cannot be changed, because the only taxlabel(s) have been assigned. NTAX must be specified before TAXLABELS command 80{ T`
DpE`Eb0F`eQEEPaPU]V0~` PGPai~ P ONPO P[XpV}@00NTplPrTPNT`l@r19NxsTaxaBlockFactory g 12NxsTaxaBlock gD`g | 3, 15NxsTaxaBlockAPI ``
DpE`Eb0F`ePEOEEPa^U]V0~ PG@E`P'[(){}"-]/\,;:=*`+<> Unexpected ; Expecting = after subcommand of the in Unexpected end-of-file while reading (end-of-file inside comment) command, but found Command option ( ) repeated in the Expecting an = after the command option of the Expecting a value after = in the (end-of-file inside ' quoted token that started on line (end-of-file inside " quoted statement) (end-of-file inside {} braced statement) Expecting ';' to terminate the must be a number greater than 0. Found Expecting a ( to begin another row of values in the Expecting a ) to end the list of values for the Expecting a value after the = sign in the @Pа8NxsToken f4../.././ncl/nxstreesblock.cpp i < trees.size() [&&NHX no trees
one tree
token.Equals("(") currNd Found a name Taxon number (coded by the token " character. Found " root taxon information no trees one tree ( unrooted ,default tree) TREE = [& !rc.empty() rc[0] == subRoot formerSib != subRoot rOtherChild Reroot failed. Leaf number was not found in the tree. Unknown taxon with a redirection to BEGIN TREES UTREE TRANSLATE BEGIN TREES;
taxIndex != (2147483647 * 2U + 1U) A tree description must be processed by ProcessTree before calling NxsSimpleTree::NxsSimpleTree Semicolon found before the end of the tree description. This means that more "(" characters than ")" were found. Expecting a number as a branch length. Found Expecting a taxon number greater than 1. Found Expecting a ( to start the tree description, but found End of tree description. Expected ; but found ( Expecting a , before a new subtree definition:
")("
"name(" and
"branch-length("
are prohibited. Expecting a branch length after a : but found ( End of tree description. Expected ; but found ) Expecting a clade description before the subtree's closing )
"()" and ",)" are prohibited. Found a : separator for a subtree at an inappropriate location. A colon is only permitted after a clade name or )-symbol. Found a : separator after a taxset name. Branch lengths cannot be assigned to multi-taxon taxsets. Found a empty subclade found. The combination "(," is prohibited. Found a empty subclade found. The combination ",," is prohibited. Found a , when a branch length was expected found. The combination ":," is prohibited. which should be preceded by a ( or a , ) has already been encountered in this tree. Duplication of taxa in a tree is prohibited. Expecting a Taxon label after a " " but this is not a recognized taxon label. (one of the members of the taxset Expecting a taxon index in a tree description, but found after tree name in TREE command ] is not a valid command comment in a TREE command Expecting command comment or tree description in TREE (or UTREE) command, but found Unexpected end of file in tree description.
This probably indicates that the parentheses in the newick description are not balanced, and one or more closing parentheses are needed. ndToDist.find(currChild) != ndToDist.end() iRow == pairwiseDist.end() || (iRow->second.find(jIndex) == iRow->second.end()) jRow == pairwiseDist.end() || (jRow->second.find(iIndex) == jRow->second.end()) WriteTreesCommand block cannot be called while the Trees Block is still being constructed in TRANSLATE command.
The translate key has NOT been added to the translation table! TRANSLATE command overwriting the taxon Expecting a , or ; after a translate key-value pair. Found A Taxa block must be read before the Trees block can be read. A TAXA block should be read before the TREES block (but no TAXA block was found). Taxa will be inferred from their usage in the TREES block. Taxa block must be read before the Trees block can be read. Expecting a tree description, but found " TRANSLATE command must precede any TREE commands in a TREES block Only one TRANSLATE command may be read in a TREES block P`p Р
DpE`Eb0Fe EPapUV0~& PG 0 ! "h" p0$pz (` $`zp
` P Zdp20NxsTreesBlockFactory g813NxsTreesBlock g\ 30 g | 3, 16NxsTreesBlockAPI virtual NxsString NxsTreesBlock::GetTranslatedTreeDescription(unsigned int) void NxsTreesBlock::HandleTreeCommand(NxsToken&, bool) void NxsTreesBlock::WriteTranslateCommand(std::ostream&) const const NxsFullTreeDescription& NxsTreesBlock::GetFullTreeDescription(unsigned int) const void NxsTreesBlock::ReplaceTaxaBlockPtr(NxsTaxaBlockAPI*) void NxsSimpleTree::Initialize(const NxsFullTreeDescription&) std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > NxsSimpleTree::GetDblPathDistances(bool) const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > NxsSimpleTree::GetIntPathDistances(bool) const void NxsSimpleNode::WriteAsNewick(std::ostream&, bool) const void NxsSimpleTree::FlipRootsChildToRoot(NxsSimpleNode*)
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init.c initfini.c crtstuff.c __CTOR_LIST__ __DTOR_LIST__ __JCR_LIST__ __do_global_dtors_aux completed.6635 dtor_idx.6637 frame_dummy __CTOR_END__ __FRAME_END__ __JCR_END__ __do_global_ctors_aux adaptation.cpp _GLOBAL__I__ZN10AdaptationC2EPK17GeneralGamlConfig _ZStL8__ioinit bipartition.cpp _GLOBAL__I__ZN11Bipartition7nBlocksE condlike.cpp _GLOBAL__I__ZN13CondLikeArrayD2Ev configoptions.cpp _GLOBAL__I__ZN17GeneralGamlConfigC2Ev configreader.cpp _GLOBAL__I__ZN12ConfigReader7UNKNOWNE datamatr.cpp _GLOBAL__I__ZN10DataMatrixD2Ev funcs.cpp _GLOBAL__I__Z19FloatingPointEqualsddd garlimain.cpp _GLOBAL__I_outman garlireader.cpp _GLOBAL__I__ZN12MyNexusTokenC2ERSi _ZGVZN11GarliReader11GetInstanceEvE2gr _ZZN11GarliReader11GetInstanceEvE2gr individual.cpp _GLOBAL__I__ZN10IndividualC2Ev linalg.cpp _ZL4CDivddddPdS_ _ZL7EigenRGiPPdS_S_S0_PiS_ _ZZL7EigenRGiPPdS_S_S0_PiS_E3is2 _ZZL7EigenRGiPPdS_S_S0_PiS_E3is1 model.cpp _GLOBAL__I_ProfCalcPmat mpifuncs.cpp optimization.cpp _GLOBAL__I_ProfIntDeriv population.cpp _GLOBAL__I_memLevel _ZZN10Population32VariableStartingTreeOptimizationEvE5C.807 rng.cpp _GLOBAL__I_rnd _ZZN3rng5gamlnEdE3ndx _ZZN3rng5gamlnEdE1t _ZZN3rng5gamlnEdE2rx _ZZN3rng5gamlnEdE3rxx _ZZN3rng5gamlnEdE2px _ZZN3rng5gamlnEdE2dx _ZZN3rng5gamlnEdE3nxm _ZZN3rng5gamlnEdE3i__ _ZZN3rng5gamlnEdE2qx _ZZN3rng5gamlnEdE4dgam _ZZN3rng5gamlnEdE2xx _ZZN3rng5gamlnEdE3gln _ZZN3rng5gamlnEdE3sum sequencedata.cpp _GLOBAL__I__ZN14NucleotideData18CalcEmpiricalFreqsEv set.cpp topologylist.cpp _GLOBAL__I__ZN12TopologyList14ntoposexaminedE translatetable.cpp _GLOBAL__I__ZN14TranslateTable12SetTaxonNameEiPKc tree.cpp _GLOBAL__I_ProfIntInt treenode.cpp _GLOBAL__I__ZN8TreeNodeC2Ei mpitrick.cpp nxsassumptionsblock.cpp _GLOBAL__I__ZN24NxsTransformationManager5ResetEv _ZZNK19NxsAssumptionsBlock18TaxonLabelToNumberE9NxsStringE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock19ReplaceTaxaBlockPtrEP15NxsTaxaBlockAPIE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock10ApplyExsetE9NxsStringE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock14ReadCharsetDefE9NxsStringR8NxsTokenbE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock14ReadTreesetDefE9NxsStringR8NxsTokenbE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock13ReadTaxsetDefE9NxsStringR8NxsTokenbE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock12ReadExsetDefE9NxsStringR8NxsTokenbE19__PRETTY_FUNCTION__ _ZZN8NxsBlock16ReadPartitionDefERSt4listISt4pairISsSt3setIjSt4lessIjESaIjEEESaIS7_EER23NxsLabelToIndicesMapperRKSsPKcSG_R8NxsTokenbbbE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock19HandleTreePartitionER8NxsTokenE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock18HandleTaxPartitionER8NxsTokenE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock13HandleOptionsER8NxsTokenE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock19HandleCharPartitionER8NxsTokenE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock17HandleCodonPosSetER8NxsTokenE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock13HandleCodeSetER8NxsTokenE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock13HandleTypeSetER8NxsTokenE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock14HandleUserTypeER8NxsTokenE19__PRETTY_FUNCTION__ _ZZN19NxsAssumptionsBlock15HandleWeightSetER8NxsTokenE19__PRETTY_FUNCTION__ nxsblock.cpp _GLOBAL__I__ZN23NxsLabelToIndicesMapper18GetIndicesFromSetsERKSsPSt3setIjSt4lessIjESaIjEERKSt3mapI9NxsStringS6_S3_IS9_ESaISt4pairIKS9_S6_EEE nxscharactersblock.cpp _GLOBAL__I__ZN15NxsCodonTripletC2EPKc _ZL11lcBaseToIndc _ZZN18NxsCharactersBlock26CodonPosPartitionToPosListERKSt4listISt4pairISsSt3setIjSt4lessIjESaIjEEESaIS7_EEPS0_IiSaIiEEE19__PRETTY_FUNCTION__ _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.216 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.217 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.218 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.219 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.220 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.221 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.222 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.223 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.224 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.225 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.226 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.227 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.228 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.229 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.230 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.231 _ZZ24getToCodonRecodingMapper19NxsGeneticCodesEnumE5C.232 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.234 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.235 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.236 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.240 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.241 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.242 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.237 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.238 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.239 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.243 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.244 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.245 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.246 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.247 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.248 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.249 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.250 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.251 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.255 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.256 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.257 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.279 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.280 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.281 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.252 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.253 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.254 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.258 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.259 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.260 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.261 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.262 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.263 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.264 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.265 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.266 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.267 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.268 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.269 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.270 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.271 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.272 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.282 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.283 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.284 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.273 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.274 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.275 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.276 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.277 _ZZ22getCodonRecodingStruct19NxsGeneticCodesEnumE5C.278 _ZZNK18NxsCharactersBlock15NumAmbigInTaxonEjPKSt3setIjSt4lessIjESaIjEEbbE19__PRETTY_FUNCTION__ _ZZN18NxsCharactersBlock15HandleEliminateER8NxsTokenE19__PRETTY_FUNCTION__ _ZZN25NxsDiscreteDatatypeMapper20StateCodeForStateSetERKSt3setIiSt4lessIiESaIiEEbbcE19__PRETTY_FUNCTION__ _ZZN25NxsDiscreteDatatypeMapper30StateCodeForNexusMultiStateSetEcRKSsR8NxsTokenjjPKSt6vectorIiSaIiEERK9NxsStringE19__PRETTY_FUNCTION__ _ZZN25NxsDiscreteDatatypeMapper38StateCodeForNexusPossibleMultiStateSetEcRKSsR8NxsTokenjjPKSt6vectorIiSaIiEERK9NxsStringE19__PRETTY_FUNCTION__ _ZZN18NxsCharactersBlock23HandleNextDiscreteStateER8NxsTokenjjRSt6vectorIiSaIiEER25NxsDiscreteDatatypeMapperPKS4_RK9NxsStringE19__PRETTY_FUNCTION__ _ZZNK25NxsDiscreteDatatypeMapper18GetStateSetForCodeEiE19__PRETTY_FUNCTION__ _ZZNK25NxsDiscreteDatatypeMapper13IsPolymorphicEiE19__PRETTY_FUNCTION__ _ZZNK25NxsDiscreteDatatypeMapper27WriteStateCodeAsNexusStringERSoibE19__PRETTY_FUNCTION__ _ZZNK18NxsCharactersBlock15ShowStateLabelsERSojjjE19__PRETTY_FUNCTION__ _ZZNK18NxsCharactersBlock26WriteStatesForTaxonAsNexusERSojjjE19__PRETTY_FUNCTION__ _ZZN18NxsCharactersBlock12GetNumStatesEjjE19__PRETTY_FUNCTION__ _ZZN18NxsCharactersBlock13IsPolymorphicEjjE19__PRETTY_FUNCTION__ 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