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Start Your TrialThis interface is used to create the garli.conf file required to run GARLI. You can specify a garli.conf file in the GARLI2 interface.
tool=GARLI_CONF_CREATOR
Input files:
infile_ - Primary Input File
Visible parameters:
is_partitioned_ - Switch - The input is a Nexus file that specifies at least two partitions (no default)
linkmodels_ - Switch - I would like to evaluate all partitions under a single model (default=0)
configure_partitions_ - Switch - I would like to specify model parameters for each partition (default=0)
numparts_ - Integer - How many partitions does your data set have? 2-5 allowed.
subsetspecificrates_ - Switch - Infer overall rate multipliers for each data partition (default=0)
Section: model
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datatype_value_ - Excl - The type of data (datatype) nucloetide (default), aminoacid, codon-aminoacid, codon
geneticcode_value_ - Excl - Select the Genetic Code (geneticcode) standard (default), vertmito, invertmito
Section: model_nucleotide
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d_ratematrix_ - Excl - Rate Matrix (ratematrix) 1rate (All Rates Equal, 2rate (HKY), 6rate (General time-reversible; default), fixed (fixed rate), custom_string (User Specified)
ACsubrates_ - String - User specified AC substitution rates (custom ratematrix) (no default)
AGsubrates_ - String - User specified AG substitution rates (custom ratematrix) (no default)
ATsubrates_ - String - User specified AT substitution rates (custom ratematrix) (no default)
CGsubrates_ - String - User specified CG substitution rates (custom ratematrix) (no default)
CTsubrates_ - String - User specified CT subsitution rates (custom ratematrix) (no default)
GTsubrates_ - String - User specified GT substitution rates (custom ratematrix) (no default)
d_statefrequencies_ - Excl - Base Frequencies (statefrequencies) equal, empircal, estimate (default), fixed
d_invariantsites_ - Excl - Proportion of invariant sites (invariantsites) none, estimate (default)
d_ratehetmodel_ - Excl - The model of rate heterogeneity (ratehetmodel) none, gamma (default)
d_numratecats_ - Integer - Number of rate categories (numratecats) default=4
Section: model_protein
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p_ratematrix_ - Excl - Protein Rate Matrix (ratematrix) poisson, jones, dayhoff, wag (default), mtmam, mtrev
p_statefrequencies_ - Excl - Amino Acid Frequencies (statefequencies) equal, empirical (default), estimate, fixed, jones, wag, mtmam, mtrev
p_invariantsites_ - Excl - Proportion of invariable sites (invariantsites) none, estimate (default)
p_ratehetmodel_ - Excl - Model of rate heterogeneity (ratehetmodel) none, gamma (default)
p_numratecats_ - Integer - Number of rate categories (numratecats; set at no more than 8) default=4
Section: model_codon
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c_ratematrix_ - Excl - Codon Rate Matrix (ratematrix) 1rate (All Rates Equal, 2rate (HKY), 6rate (General time-reversible; default), fixed (fixed rate), custom_string (User Specified)
c_statefrequencies_ - Excl - Codon Frequencies (statefequencies) equal, empirical, f1x4, f3x4 (default)
c_ratehetmodel_ - Excl - dN/dS categories (or Omega) (ratehetmodel) none, nonsynonymous (default)
c_numratecats_ - Integer - Number of dN/dS parameter categories (numratecats) (default=3)
Section: model1 (see Section Model above)
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datatype_value1_ - Excl - The type of data (datatype)
geneticcode_value1_ - Excl - Select the Genetic Code (geneticcode)
Section: model_nucleotide1 (see model nucleotide section above)
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d_ratematrix1_ - Excl - Rate Matrix (ratematrix)
ACsubrates1_ - String - User specified AC substitution rates (custom ratematrix)
AGsubrates1_ - String - User specified AG substitution rates (custom ratematrix)
ATsubrates1_ - String - User specified AT substitution rates (custom ratematrix)
CGsubrates1_ - String - User specified CG substitution rates (custom ratematrix)
CTsubrates1_ - String - User specified CT subsitution rates (custom ratematrix)
GTsubrates1_ - String - User specified GT substitution rates (custom ratematrix)
d_statefrequencies1_ - Excl - Base Frequencies (statefrequencies)
d_invariantsites1_ - Excl - Proportion of invariant sites (invariantsites)
d_ratehetmodel1_ - Excl - The model of rate heterogeneity (ratehetmodel)
d_numratecats1_ - Integer - Number of rate categories (numratecats)
Section: model_protein1 (see model protein section above)
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p_ratematrix1_ - Excl - Protein Rate Matrix (ratematrix)
p_statefrequencies1_ - Excl - Amino Acid Frequencies (statefequencies)
p_invariantsites1_ - Excl - Proportion of invariable sites (invariantsites)
p_ratehetmodel1_ - Excl - Model of rate heterogeneity (ratehetmodel)
p_numratecats1_ - Integer - Number of rate categories (numratecats; set at no more than 8)
Section: model_codon1 (see model codon section above)
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c_ratematrix1_ - Excl - Codon Rate Matrix (ratematrix)
c_statefrequencies1_ - Excl - Codon Frequencies (statefequencies)
c_ratehetmodel1_ - Excl - dN/dS categories (or Omega) (ratehetmodel)
c_numratecats1_ - Integer - Number of dN/dS parameter categories (numratecats)
Section: model2 (see model section above)
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datatype_value2_ - Excl - The type of data (datatype)
geneticcode_value2_ - Excl - Select the Genetic Code (geneticcode)
Section: model_nucleotide2 (see model nucleotide section above)
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d_ratematrix2_ - Excl - Rate Matrix (ratematrix)
ACsubrates2_ - String - User specified AC substitution rates (custom ratematrix)
AGsubrates2_ - String - User specified AG substitution rates (custom ratematrix)
ATsubrates2_ - String - User specified AT substitution rates (custom ratematrix)
CGsubrates2_ - String - User specified CG substitution rates (custom ratematrix)
CTsubrates2_ - String - User specified CT subsitution rates (custom ratematrix)
GTsubrates2_ - String - User specified GT substitution rates (custom ratematrix)
d_statefrequencies2_ - Excl - Base Frequencies (statefrequencies)
d_invariantsites2_ - Excl - Proportion of invariant sites (invariantsites)
d_ratehetmodel2_ - Excl - The model of rate heterogeneity (ratehetmodel)
d_numratecats2_ - Integer - Number of rate categories (numratecats)
Section: model_protein2 (see model protein section above)
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p_ratematrix2_ - Excl - Protein Rate Matrix (ratematrix)
p_statefrequencies2_ - Excl - Amino Acid Frequencies (statefequencies)
p_invariantsites2_ - Excl - Proportion of invariable sites (invariantsites)
p_ratehetmodel2_ - Excl - Model of rate heterogeneity (ratehetmodel)
p_numratecats2_ - Integer - Number of rate categories (numratecats; set at no more than 8)
Section: model_codon2 (see model codon section above)
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c_ratematrix2_ - Excl - Codon Rate Matrix (ratematrix)
c_statefrequencies2_ - Excl - Codon Frequencies (statefequencies)
c_ratehetmodel2_ - Excl - dN/dS categories (or Omega) (ratehetmodel)
c_numratecats2_ - Integer - Number of dN/dS parameter categories (numratecats)
Section: model3 (see model section above)
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datatype_value3_ - Excl - The type of data (datatype)
geneticcode_value3_ - Excl - Select the Genetic Code (geneticcode)
Section: model_nucleotide3 (see model nucleotide section above)
*************************************************************************************
d_ratematrix3_ - Excl - Rate Matrix (ratematrix)
ACsubrates3_ - String - User specified AC substitution rates (custom ratematrix)
AGsubrates3_ - String - User specified AG substitution rates (custom ratematrix)
ATsubrates3_ - String - User specified AT substitution rates (custom ratematrix)
CGsubrates3_ - String - User specified CG substitution rates (custom ratematrix)
CTsubrates3_ - String - User specified CT subsitution rates (custom ratematrix)
GTsubrates3_ - String - User specified GT substitution rates (custom ratematrix)
d_statefrequencies3_ - Excl - Base Frequencies (statefrequencies)
d_invariantsites3_ - Excl - Proportion of invariant sites (invariantsites)
d_ratehetmodel3_ - Excl - The model of rate heterogeneity (ratehetmodel)
d_numratecats3_ - Integer - Number of rate categories (numratecats)
Section: model_protein3 (see model protein section above)
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p_ratematrix3_ - Excl - Protein Rate Matrix (ratematrix)
p_statefrequencies3_ - Excl - Amino Acid Frequencies (statefequencies)
p_invariantsites3_ - Excl - Proportion of invariable sites (invariantsites)
p_ratehetmodel3_ - Excl - Model of rate heterogeneity (ratehetmodel)
p_numratecats3_ - Integer - Number of rate categories (numratecats; set at no more than 8)
Section: model_codon3 (see model codon section above)
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c_ratematrix3_ - Excl - Codon Rate Matrix (ratematrix)
c_statefrequencies3_ - Excl - Codon Frequencies (statefequencies)
c_ratehetmodel3_ - Excl - dN/dS categories (or Omega) (ratehetmodel)
c_numratecats3_ - Integer - Number of dN/dS parameter categories (numratecats)
Section: model4 (see model section above)
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datatype_value4_ - Excl - The type of data (datatype)
geneticcode_value4_ - Excl - Select the Genetic Code (geneticcode)
Section: model_nucleotide4 (see model nucleotide section above)
*************************************************************************************
d_ratematrix4_ - Excl - Rate Matrix (ratematrix)
ACsubrates4_ - String - User specified AC substitution rates (custom ratematrix)
AGsubrates4_ - String - User specified AG substitution rates (custom ratematrix)
ATsubrates4_ - String - User specified AT substitution rates (custom ratematrix)
CGsubrates4_ - String - User specified CG substitution rates (custom ratematrix)
CTsubrates4_ - String - User specified CT subsitution rates (custom ratematrix)
GTsubrates4_ - String - User specified GT substitution rates (custom ratematrix)
d_statefrequencies4_ - Excl - Base Frequencies (statefrequencies)
d_invariantsites4_ - Excl - Proportion of invariant sites (invariantsites)
d_ratehetmodel4_ - Excl - The model of rate heterogeneity (ratehetmodel)
d_numratecats4_ - Integer - Number of rate categories (numratecats)
Section: model_protein4 (see model protein section above)
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p_ratematrix4_ - Excl - Protein Rate Matrix (ratematrix)
p_statefrequencies4_ - Excl - Amino Acid Frequencies (statefequencies)
p_invariantsites4_ - Excl - Proportion of invariable sites (invariantsites)
p_ratehetmodel4_ - Excl - Model of rate heterogeneity (ratehetmodel)
p_numratecats4_ - Integer - Number of rate categories (numratecats; set at no more than 8)
Section: model_codon4 (see model codon section above)
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c_ratematrix4_ - Excl - Codon Rate Matrix (ratematrix)
c_statefrequencies4_ - Excl - Codon Frequencies (statefequencies)
c_ratehetmodel4_ - Excl - dN/dS categories (or Omega) (ratehetmodel)
c_numratecats4_ - Integer - Number of dN/dS parameter categories (numratecats)
Section: model5 (see model section above)
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datatype_value5_ - Excl - The type of data (datatype)
geneticcode_value5_ - Excl - Select the Genetic Code (geneticcode)
Section: model_nucleotide5 (see model nucleotide section above)
*************************************************************************************
d_ratematrix5_ - Excl - Rate Matrix (ratematrix)
ACsubrates5_ - String - User specified AC substitution rates (custom ratematrix)
AGsubrates5_ - String - User specified AG substitution rates (custom ratematrix)
ATsubrates5_ - String - User specified AT substitution rates (custom ratematrix)
CGsubrates5_ - String - User specified CG substitution rates (custom ratematrix)
CTsubrates5_ - String - User specified CT subsitution rates (custom ratematrix)
GTsubrates5_ - String - User specified GT substitution rates (custom ratematrix)
d_statefrequencies5_ - Excl - Base Frequencies (statefrequencies)
d_invariantsites5_ - Excl - Proportion of invariant sites (invariantsites)
d_ratehetmodel5_ - Excl - The model of rate heterogeneity (ratehetmodel)
d_numratecats5_ - Integer - Number of rate categories (numratecats)
Section: model_protein5 (see model protein section above)
*************************************************************************************
p_ratematrix5_ - Excl - Protein Rate Matrix (ratematrix)
p_statefrequencies5_ - Excl - Amino Acid Frequencies (statefequencies)
p_invariantsites5_ - Excl - Proportion of invariable sites (invariantsites)
p_ratehetmodel5_ - Excl - Model of rate heterogeneity (ratehetmodel)
p_numratecats5_ - Integer - Number of rate categories (numratecats; set at no more than 8)
Section: model_codon5 (see model codon section above)
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c_ratematrix5_ - Excl - Codon Rate Matrix (ratematrix)
c_statefrequencies5_ - Excl - Codon Frequencies (statefequencies)
c_ratehetmodel5_ - Excl - dN/dS categories (or Omega) (ratehetmodel)
c_numratecats5_ - Integer - Number of dN/dS parameter categories (numratecats)
Section: model_trees
*************************************************************************************
streefname_choose_ - Excl - Specify where the starting tree topology comes from (streefname) random, stepwise (default), upload
attachments_val_ - Integer - Specify the number of attachment branches evaluated for each taxon (attachmentspertaxon) (default=50)
searchreps_value_ - Integer - Specify the number of independent search replicates to perform during a program execution.(searchreps) (default=2)
bootstrapreps_ - Integer - Bootstrap Repetitions (-bootstrapreps) (default=0)
outgroup_tax_ - String - Outgroup taxa numbers, separated by spaces (outgroup) (no default)
collapsebranches_g_ - Switch - Collapse minimum length branches (effectively zero length) branch upon output of the final tree. (default=0)
constraintfile_ - Switch - I want to use a Constraint File (constraintfile; Newick format) (default=0)
Section: model_initialization
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refinestart_ - Switch - Perform Initial Rough Optimization (refinestart) (default=1)
randseed_ - Integer - Random Seed ( -1 means it will be chosen for you) (default=-1)
Section: algorithm_population
*************************************************************************************
selectionintensity_ - Float - Selection Intensity (0.01 to 5.0) (selectionintensity) (default=0.5)
nindivs_ - Integer - Number of Individuals (nindivs 2 to 100) (default=4)
Section: algorithm_brlen
*************************************************************************************
startoptprec_ - Float - Starting Precision (startoptprec: 0.005 - 5.0) (default=0.5)
minoptprec_ - Float - Minimum Precision (minoptprec: 0.001 - 0.01) (default=0.01)
numberofprecreductions_ - Integer - Number of Precision Reductions (0 - 100) (default=20)
Section: algorithm_mutation_prior_weighting
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modweight_ - Float - Model Mutations (modweight) (default=0.5)
brlenweight_ - Float - Branch-length Mutations (brlenweight) (default=0.2)
topoweight_ - Float - All Topology Mutations (topoweight) (default=1.0)
randnniweight_ - Float - NNI Mutations (randnniweight) (default=0.1)
randsprweight_ - Float - SPR Mutations (randsprweight) (default=0.3)
limsprweight_ - Float - Limited SPR Mutations (limsprweight) (default=0.6)
Section: algorithm_mutation_details
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limsprrange_ - Integer - Max Limited SPR Branch Movement (limsprrange) (default=6)
uniqueswapbias_ - Float - Unique Swap Bias (uniqueswapbias)(default=0.1)
Section: general_logs
*************************************************************************************
saveevery_g_ - Integer - Save best tree with interval (saveevery) (default=100)
outputcurrentbesttopology_ - Switch - Output current best tree at "savevery" interval (outputcurrentbesttopology) (no default)
logevery_g_ - Integer - Save best score with interval (logevery) (default=10)
outputeachbettertopology_g_ - Switch - Save each improved topology (outputeachbettertopology; can result in a very large file) (default=0)
inferinternalstateprobs_g_ - Switch - Output state probabilities of internal nodes (inferinternalstateprobs) (default=0)
outputphyliptree_g_ - Switch - Output PHYLIP-format tree (outputphyliptree) (default=0)
outputmostlyuselessfiles_g_ - Switch - Output files of questionable utility (default=0)
Section: general_run
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enforcetermconditions_ - Switch - Automatically terminate run (enforcetermconditions; recommended) (default=1)
genthreshfortopoterm_ - Integer - Generations without improving topology (genthreshfortopoterm) (default=20000)
significanttopochange_ - Float - lnL increase for significantly better topology (significanttopochange) (default=0.01)
scorethreshforterm_ - Float - Score improvement threshold (scorethreshforterm) (default=0.05)
stopgen_ - Integer - Limit generations to maximum of (stopgen) (default=214783646)
stoptime_ - Integer - Limit run time to maximum of (stoptime, in seconds) (default=214783646)
resampleproportion_ - Float - Resampling where the pseudoreplicate datasets have a different number of alignment columns than the real data (resampleproportion) (default=1.0)