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Start Your TrialThis interface is used from the REST API to convey input files, and configure the GARLI v.2 parameters. GARLI parameters are delivered through a file named garli.conf, which is created by the CIPRES application using the selections made through this interface. The user is also allowed to upload their own garli.conf file, which may be created by the user, or via garli_conf_creator.
The Tool ID for this interface is GARLI2_TGB. It is selected with tool=GARLI2_TGB
Supported parameters: Input files:
input.infile_ - Primary Input File
input.upload_conffile_ - InFile - Select the GARLI configuration file
input.streefname_userdata_ - InFile - Choose a Starting Tree (streefname file)
input.constraintfile_control_ - InFile - Choose a Constraint File in Newick Format (constraintfile)
Supported parameters:
vparam.runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly) (default=0.5, max=168)
These switches are used to try to help the user find documentation for an uploaded garli-conf file, which is somewhat non-obvious.
vparam.user_conffile_ - Switch - I would like to provide my own GARLI configuration file (for help, see the GARLI.conf Creator tool) (no default). When the value is set to 1, most other options are disabled.
vparam.userconffilehere_ - Switch - The garli.conf file was created using GARLI.conf Creator or the GARLI2_TG interface (no default)
vparam.userconffilethere_ - Switch - The garli.conf file was created outside of CIPRES (no default)
vparam.userconffileconfirm_ - Switch - I have set the values of searchreps and bootstrapreps correctly (no default)
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configure_partitions
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is_partitioned_ - Switch - The input is a Nexus file that specifies at least two partitions (no default)
linkmodels_ - Switch - Apply selected model parameters to all partitions. only if is_partitioned_=1.
subsetspecificrates_ - Switch - Infer overall rate multipliers for each data partition. (default=0)
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run_configuration
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streefname_choose_ - Excl - Specify where the starting tree topology comes from (streefname) allowed: random, stepwise, upload (default=stepwise)
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) Set this up to 96. (default=2)
bootstrapreps_ - Integer - Bootstrap Repetitions (-bootstrapreps) default=0; maximum=100.
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).
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model initialization
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refinestart_ - Switch - Perform Initial Rough Optimization (refinestart) default=1
randseed_ - Integer - Random Seed (default -1 means it will be chosen for you)
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model
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datatype_value_ - Excl - The type of data (datatype) nucleotide, aminoacid, codon-aminoacid, codon. default=nucleotide
geneticcode_value_ - Excl - Select the Genetic Code (geneticcode) standard (default), vertmito, invertmito
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model_nucleotide
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d_ratematrix_ - Excl - Rate Matrix (ratematrix) allowed none; gamma (default)
ACsubrates_ - String - User specified AC substitution rates (custom ratematrix)
AGsubrates_ - String - User specified AG substitution rates (custom ratematrix)
ATsubrates_ - String - User specified AT substitution rates (custom ratematrix)
CGsubrates_ - String - User specified CG substitution rates (custom ratematrix)
CTsubrates_ - String - User specified CT substitution rates (custom ratematrix)
GTsubrates_ - String - User specified GT substitution rates (custom ratematrix)
d_statefrequencies_ - Excl - Base Frequencies (statefrequencies) equal, empirical, 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
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model_protein
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p_ratematrix_ - Excl - Protein Rate Matrix (ratematrix)
p_statefrequencies_ - Excl - Amino Acid Frequencies (statefequencies)
p_invariantsites_ - Excl - Proportion of invariable sites (invariantsites)
p_ratehetmodel_ - Excl - Model of rate heterogeneity (ratehetmodel)
p_numratecats_ - Integer - Number of rate categories (numratecats; set at no more than 8)
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model_codon
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c_ratematrix_ - Excl - Codon Rate Matrix (ratematrix) 1rate, 2rate (default), 6rate, fixed, custom, string
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)
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algorithm_population
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selectionintensity_ - Float - Selection Intensity (0.01 to 5.0) (selectionintensity)
nindivs_ - Integer - Number of Individuals (nindivs 2 to 100)
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algorithm_brlen
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startoptprec_ - Float - Starting Precision (startoptprec: 0.005 - 5.0)
minoptprec_ - Float - Minimum Precision (minoptprec: 0.001 - 0.01)
numberofprecreductions_ - Integer - Number of Precision Reductions (0 - 100)
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algorithm_mutation_prior_weighting
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modweight_ - Float - Model Mutations (modweight) default=0.05
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
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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
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general_logs
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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 fate, problog, and swaplog files. default=0
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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_ - Switch - Use Resampling where the pseudoreplicate datasets have a different number of alignment columns than the real data (resampleproportion) no default
resampleproportion_val_ - Float - Enter the value for resampling proportion (resampleproportion) default=1.0
. Please let us know if you have any problems with the documentation.