RAxML HPC2 TGB REST


RAxML interface: raxmlhpc2__tgb

This is one of several RAxML interfaces that can be used from the REST API. Others include raxmlhpc2_tgb.xml, raxmlhpc2bb.xml, raxmlhpc8_rest_xsede.xml, and raxmlhpc2_workflow.xml. This interface is a supported legacy interface. If you are starting a new client or service, please use raxmlhpc8_rest_xsede.xml. It will be much easier to use.

The tool id for this interface is RAXMLHPC2_TGB. It is selected with toolId=RAXMHPC2__TGB

Supported parameters for tool=RAXMLHPC2_TGB that require input files (prefix with "input.") are:
input.infile_ - InFile - Primary Input File
input.treetop_ - InFile - Supply a tree (Not available when doing rapid bootstrapping, -x) (-t)
input.binary_backbone_ - InFile - Binary Backbone (-r)
input.partition_ - InFile - Use a mixed/partitioned model? (-q)
input.exclude_file_ - InFile - Choose an input file that excludes the range of positions specifed in this file (-E)
input.set_weights_ - InFile - Weight characters as specifed in this file (-a)
input.constraint_ - InFile - Constraint (-g)
input.bunchotops_ - InFile - File with topologies for bipartitions or bootstopping (-z)
input.apo_tops_ - InFile - File with topologies for a posteriori bootstopping (-z) only when use_apobootstopping_=1.

input.user_prot_matrix_ - InFile - (datatype=protein) Upload a Custom Protein Substitution Matrix (-P)
input.user_prot_matrixq1_ - InFile - (datatype=protein; mulcustom_aa_matrices_=1) Select the First Protein Substitution Matrix Called in Your Partition File.
input.user_prot_matrixq2_ - InFile - (datatype=protein, and user_prot_matrixq1_ ) Select the Second Protein Substitution Matrix Called in Your Partition File.
input.user_prot_matrixq3_ - InFile - (datatype=protein and user_prot_matrixq2_ ) Select the Third Protein Substitution Matrix Called in Your Partition File.
input.user_prot_matrixq4_ - InFile - (datatype=protein and user_prot_matrixq3_) Select the Fourth Protein Substitution Matrix Called in Your Partition File.
input.user_prot_matrixq5_ - InFile - (datatype=protein and user_prot_matrixq4_) Select the Fifth Protein Substitution Matrix Called in Your Partition File.

input.sec_str_file_ - InFile - (datatype=rna) Upload a Secondary Structure File (-S)

Supported parameters for tool=RAXMLHPC2_TGB (that prefix with "vparam.") are:
vparam.runtime_ - Float - Maximum Hours to Run (default = 0.25, max=168)
vparam.outsuffix_ - String - Set a name for output files (default=result)
vparam.MLsearch_CAT_ - Switch - Enable ML searches under CAT (-F) (default=0, 1=on)
vparam.more_memory_ - Switch - Use for a data set that may require more than 12.5 GB of memory (default=0, 1=on) deprecated
vparam.nchar_ - Integer - Enter the number of patterns in your dataset (only when more_memory_=1; default=1000)
vparam.ntax_ - Integer - Enter the number of taxa in your dataset (only when more_memory_=1; no default) deprecated
vparam.many_partitions_ - Swtich - My dataset has more than 100 partitions. Default=0.

vparam.datatype_ - Excl - Please select the Data Type. allowed values:protein, dna, rna, multi, bin. Default=dna.
vparam.outgroup_ - String - Outgroup (one or more comma-separated outgroups, no blank space allowed)
vparam.number_cats_ - Integer - Specify the number of distinct rate categories (-c) (default=25)
vparam.disable_ratehet_ - Switch - Disable Rate Heterogeneity (-V) (default=0, 1=on)
vparam.provide_parsimony_seed_ - Switch - Specify a random seed value for parsimony inferences (-p) (default=1, 1=on)
vparam.parsimony_seed_val_ - Integer - Enter a random seed value for parsimony inferences (gives reproducible results from random starting tree) (default=12345)
vparam.rearrangement_yes_ - Switch - Specify an initial rearrangement setting (-i) (default=0, 1=on)
vparam.number_rearrange_ - Integer - Specify the distance from original pruning point (-i) (only if rearrangement_yes_=1, no default)
vparam.estimate_perpartbrlen_ - Switch - Estimate individual per-partition branch lengths (-M) (default=0, 1=on)
vparam.ascertainment_ - Excl - Correct for Ascertainment bias (ASC_) (Allowed: ASC_ / null; default=null)
vparam.ascertainment_corr_ - Excl - Ascertainment bias correction type (--asc-corr) (allowed: lewis, stamatakis, felsenstein; default=lewis)
vparam.invariable_ - Excl - Estimate proportion of invariable sites (GTRGAMMA + I) (Allowed: I/null; default = null)
vparam.printbrlength_ - Switch - Print branch lengths (-k) (default=0, 1=on)
vparam.disable_seqcheck_ - Switch - Disable checking for sequences with no values (-O) (default=0, 1=on)
vparam.mesquite_output_ - Switch - Print output files that can be parsed by Mesquite. (-mesquite) not allowed with hybrid code because that currently fails. (default=0, 1=on)
vparam.no_bfgs_ - Switch - Don't use BFGS searching algorithm (default=0, 1 = --no-bfgs)
vparam.specify_runs_ - Switch - Specify the number alternative runs on distinct starting trees? (-#/-N), only available if bootstrapping isnt used.
vparam.altrun_number_ - Integer - Enter number of number alternative runs (-#/-N) only available if bootstrapping isnt used.
vparam.intermediate_treefiles_ - Switch - Write intermediate tree files to a file (-j) (default=0, 1=on)
vparam.convergence_criterion_ - Switch - Use ML search convergence criterion. (-D) (default=0, 1=on)

Model setting options:
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DNA sequence options
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vparam.dna_gtrcat_ - Excl - Choose model for bootstrapping phase. GTRCAT or GTRGAMMA, default=GTRCAT
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Protein sequence options
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vparam.prot_sub_model_ - Excl - Choose GAMMA or CAT model: PROTCAT or PROTGAMMA, default=PROTCAT
vparam.prot_matrix_spec_ - Excl - Protein Substitution Matrix - Values allowed: DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, LG, MTART, MTZOA, PMB, HIVB, HIVW, JTTDCMUT, FLU, DUMMY, DUMMY2, AUTO, LG4M, LG4X, PROT_FILE, GTR_UNLINKED, GTR. default=DAYHOFF
vparam.mulcustom_aa_matrices_ - Switch - Use a Partition file that specifies AA Matrices. Turns on the ability to upload 1-5 partition files. default=0 (default=0, 1=on)
vparam.use_emp_freqs_ - Excl - Use empirical frequencies? F (yes) or null (no) default=no

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RNA Secondary structure options
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vparam.rna_model_ - Excl - Use an RNA Secondary Structure Substitution Model (-A) S6A, S6B, S6C, S6D, S6E, S7A, S7B, S7C, S7D, S7E, S7F, S16A, S16B. default= S16A
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Binary Data Options
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vparam.bin_model_ - Excl - Binary data model (-m) BINCAT or BINGAMMA, default=BINCAT
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Multistate morphological data
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vparam.multi_model_ - Excl - Multiple State Data Model (-m) MULTICAT or MULTIGAMMA, default=MULTICAT
vparam.choose_multi_model_ - Excl - Select a Multiple state data model (-K) ORDERED, MK, GTR. default=GTR
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Specify the Analysis. A value of 1 turns these options on, most are mutually exclusive
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vparam.startingtreeonly_ - Switch - Only compute a randomized parsimony starting tree (-y) default=0
vparam.bipartitions_ - Switch - Draw bipartitions onto a single tree topology. (-f b) default=0
vparam.ancestral_states_ - Switch - Compute Marginal Ancestral States using a rooted reference tree. (-f A) default=0
vparam.log_likelihood_ - Switch - Compute a log likelihood test (-f h) default=0
vparam.thorough_opt_ - Switch - Do A Final Optimization of ML Tree (-f T) default=0
vparam.compute_mr_ - Switch - Compute majority rule consensus tree (-J) default=0
vparam.specify_mr_ - Excl - Specify majority rule consensus tree (-J) technique (only when compute_mr_=1) allowed values: MRE, STRICT, MR_DROP, STRICT_DROP. default=MRE
vparam.compute_ml_distances_ - Switch - Compute pair-wise ML distances (-f x; GAMMA models only) default=0
vparam.fast_tree_ - Switch - Run very fast experimental tree search (-f E) default=0
vparam.morpho_weight_calibration_ - Switch - Execute morphological weight calibration using maximum likelihood (-f u) default=0
vparam.classify_into_reftree_ - Switch - Classify a bunch of environmental sequences into a reference tree using thorough read insertions(-f v) default=0

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Bootstrapping Options
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vparam.mulparambootstrap_seed_ - Switch - Conduct Multiparametric Bootstrapping? (-b) (not allowed if bootstrap_seed_=1) default=0
vparam.mulparambootstrap_seed_val_ - Integer - Enter a random seed value for multi-parametric bootstrapping (only when mulparambootstrap_seed_=1) default=12345.
vparam.bootstrap_seed_ - Switch - Conduct rapid bootstrapping? (-x) (not allowed if mulparambootstrap_seed_=1) no default.
vparam.bootstrap_seed_val_ - Integer - Enter a random seed value for rapid bootstrapping (only when bootstrap_seed_=1) default=12345.
vparam.mlsearch_ - Switch - Conduct a rapid Bootstrap analysis and search for the best-scoring ML tree in one single program run. (-f a) (requires bootstrap_seed_=1) default=1
vparam.specify_bootstraps_ - Switch - Specify an Explicit Number of Bootstraps (only when bootstrap_seed_=1 or mulparambootstrap_seed_=1) default=1
vparam.bootstop_ - Integer - Bootstrap iterations (-#|-N) (from 1 to 1000; default = 100)
vparam.use_bootstopping_ - Switch - Let RAxML halt bootstrapping automatically (not allowed when specify_bootstraps_=1) default=0
vparam.freq_bootstopping_ - Switch - Stop Bootstrapping Automatically with Frequency Criterion (only if use_bootstopping_=1; mr_bootstopping_=0) default=0
vparam.mr_bootstopping_ - Switch - Stop Bootstrapping Automatically with Majority Rule Criterion (recommended) (only if use_bootstopping_=1; freq_bootstopping_=0) default=1
vparam.mrbootstopping_type_ - Excl - Select Majority Rule Criterion: (autoMRE is recommended) (-N) autoMR, autoMRE, autoMRE_IGN, default=autoMRE
vparam.use_apobootstopping_ - Switch - Use a posteriori bootstrapping (default=0, requires -z option upload)
vparam.aposterior_bootstopping_ - Excl - Select the criterion for a posteriori bootstopping analysis (only if use_apobootstopping_=1) allowed: autoMR, autoMRE, autoMRE_IGN, default=autoMRE

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