GARLI2_TGB
infile_ - Primary Input File
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
user_conffile_ - Switch - I would like to provide my own GARLI configuration file (for help, see the GARLI.conf Creator tool)
userconffilehere_ - Switch - The garli.conf file was created using GARLI.conf Creator or the GARLI2_TG interface
userconffilethere_ - Switch - The garli.conf file was created outside of CIPRES
upload_conffile_ - InFile - Select the GARLI configuration file
userconffileconfirm_ - Switch - I have set the values of searchreps and bootstrapreps correctly
a_matrix_file_ - Results - Input
b_command_line_ - Results - commandline
c_garli_configuration_ - Results - Input parameters
d_starting_tree_ - Results - Input starting tree/model
e_constraint_file_ - Results - Input topology constraints
f_scheduler_configuration_ - Results - Scheduling parameters
ff_scheduler_configuration_ - Results - Scheduling stderr
g_jobinfo_txt_ - Results - jobinfo_parameters
h_start_txt_ - Results - start_txt
hh_done_txt_ - Results - done_txt
i_garli_log00_results_ - Results -
j_garli_screenlog_results_ - Results -
k_garli_boottree_results_ - Results -
l_garli_allboottree_results_ - Results -
m_garli_besttree_results_ - Results -
n_garli_besttree_results_ - Results -
o_garli_bestalltree_results_ - Results -
all_results_ - Results -
Section: ****************************************************************************
configure_partitions
*************************************************************************************
is_partitioned_ - Switch - The input is a Nexus file that specifies at least two partitions
linkmodels_ - Switch - Apply selected model parameters to all partitions
subsetspecificrates_ - Switch - Infer overall rate multipliers for each data partition
Section: ****************************************************************************
run_configuration
*************************************************************************************
streefname_choose_ - Excl - Specify where the starting tree topology comes from (streefname)
streefname_userdata_ - InFile - Choose a Starting Tree (streefname file)
attachments_val_ - Integer - Specify the number of attachment branches evaluated for each taxon (attachmentspertaxon)
searchreps_value_ - Integer - Specify the number of independent search replicates to perform during a program execution.(searchreps)
bootstrapreps_ - Integer - Bootstrap Repetitions (-bootstrapreps)
outgroup_tax_ - String - Outgroup taxa numbers, separated by spaces (outgroup)
collapsebranches_g_ - Switch - Collapse minimum length branches (effectively zero length) branch upon output of the final tree
constraintfile_control_ - InFile - Choose a Constraint File in Newick Format (constraintfile)
Section: ****************************************************************************
model_initialization
*************************************************************************************
refinestart_ - Switch - Perform Initial Rough Optimization (refinestart)
randseed_ - Integer - Random Seed ( -1 means it will be chosen for you)
Section: ****************************************************************************
model
*************************************************************************************
datatype_value_ - Excl - The type of data (datatype)
geneticcode_value_ - Excl - Select the Genetic Code (geneticcode)
Section: ****************************************************************************
model_nucleotide
*************************************************************************************
d_ratematrix_ - Excl - Rate Matrix (ratematrix)
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 subsitution rates (custom ratematrix)
GTsubrates_ - String - User specified GT substitution rates (custom ratematrix)
d_statefrequencies_ - Excl - Base Frequencies (statefrequencies)
d_invariantsites_ - Excl - Proportion of invariant sites (invariantsites)
d_ratehetmodel_ - Excl - The model of rate heterogeneity (ratehetmodel)
d_numratecats_ - Integer - Number of rate categories (numratecats)
Section: ****************************************************************************
model_protein
*************************************************************************************
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)
Section: ****************************************************************************
model_codon
*************************************************************************************
c_ratematrix_ - Excl - Codon Rate Matrix (ratematrix)
c_statefrequencies_ - Excl - Codon Frequencies (statefequencies)
c_ratehetmodel_ - Excl - dN/dS categories (or Omega) (ratehetmodel)
c_numratecats_ - Integer - Number of dN/dS parameter categories (numratecats)
Section: ****************************************************************************
algorithm_population
*************************************************************************************
selectionintensity_ - Float - Selection Intensity (0.01 to 5.0) (selectionintensity)
nindivs_ - Integer - Number of Individuals (nindivs 2 to 100)
Section: ****************************************************************************
algorithm_brlen
*************************************************************************************
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)
Section: ****************************************************************************
algorithm_mutation_prior_weighting
*************************************************************************************
modweight_ - Float - Model Mutations (modweight)
brlenweight_ - Float - Branch-length Mutations (brlenweight)
topoweight_ - Float - All Topology Mutations (topoweight)
randnniweight_ - Float - NNI Mutations (randnniweight)
randsprweight_ - Float - SPR Mutations (randsprweight)
limsprweight_ - Float - Limited SPR Mutations (limsprweight)
Section: ****************************************************************************
algorithm_mutation_details
*************************************************************************************
limsprrange_ - Integer - Max Limited SPR Branch Movement (limsprrange)
uniqueswapbias_ - Float - Unique Swap Bias (uniqueswapbias)
Section: ****************************************************************************
general_logs
*************************************************************************************
saveevery_g_ - Integer - Save best tree with interval (saveevery)
outputcurrentbesttopology_ - Switch - Output current best tree at "savevery" interval (outputcurrentbesttopology)
logevery_g_ - Integer - Save best score with interval (logevery)
outputeachbettertopology_g_ - Switch - Save each improved topology (outputeachbettertopology; can result in a very large file)
inferinternalstateprobs_g_ - Switch - Output state probabilities of internal nodes (inferinternalstateprobs)
outputphyliptree_g_ - Switch - Output PHYLIP-format tree (outputphyliptree)
outputmostlyuselessfiles_g_ - Switch - Output fate, problog, and swaplog files
Section: ****************************************************************************
general_run
*************************************************************************************
enforcetermconditions_ - Switch - Automatically terminate run (enforcetermconditions; recommended)
genthreshfortopoterm_ - Integer - Generations without improving topology (genthreshfortopoterm)
significanttopochange_ - Float - lnL increase for significantly better topology (significanttopochange)
scorethreshforterm_ - Float - Score improvement threshold (scorethreshforterm)
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)
resampleproportion_val_ - Float - Enter the value for resampling proportion (resampleproportion)