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is a complete rewrite of the Evolutionary Placement Algorithm (EPA), previously implemented in RAxML. It uses libpll and pll-modules to perform maximum likelihood-based phylogenetic placement of genetic sequences on a user-supplied reference tree and alignment.
bfast
-fileIf you use EPA-ng, please cite:Pierre Barbera, Alexey M Kozlov, Lucas Czech, Benoit Morel, Diego Darriba, Tomáš Flouri, Alexandros Stamatakis, EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences, Systematic Biology, Volume 68, Issue 2, March 2019, Pages 365–369, https://doi.org/10.1093/sysbio/syy054
The Tool ID for this interface is tool=EPA_NG_XSEDE
Supported parameters:
input.infile_= Tree file in Newick format
input.ref_file_= Reference MSA file (fasta)
input.binary_file_= Alternative binary reference file
input.query_file_= Query file (fasta or bfast)
input.raxquery_file_= Model file
vparam.runtime_= - Float - Maximum Hours to Run (up to 168 hours) (default=1.0)
vparam.model_string_= - String - The model to be used by EPA (in lieu of a raxml file header, raxquery_file_ ); no default
vparam.choose_heuristic_= - Excl Choose the heuristic (dyn-heur, fix-heur, baseball-heur, no-heur)
vparam.specify_dynamic_= - Float - Provide a value for the dynamic heuristic between 0 and 1
vparam.specify_fixed_= - Float - Provide a value for the fixed heuristic between 0 and 1
vparam.specify_queryseq_= - Integer - Number of query sequences to be read in at a time. (--chunk-size)
vparam.employ_queryseq_= - Switch - Employ old style of branch length optimization during thorough insertion
vparam.no_premask_= - Switch - Do not premask sequences
vparam.rate_scalers_= Excl Use individual rate scalers? (--rate-scalers) (off,on,auto)
vparam.likelihood_weight_= Excl, Likelihood weighting filter-acc-lwr or filter-min-lwr
vparam.specify_acclw_= Float, Accumulated likelihood weight
vparam.specify_minlw_= Float, Minimum likelihood weight Default= 0.01
vparam.specify_minplace_= Integer, Minimum number of placements per sequence to include (default=1)
vparam.specify_maxplace_ = Integer, Maximum number of placements per sequence to include (default=7)
vparam.specify_precision_ = Integer, Output decimal point precision for floating point (--precision)
vparam.preserve_rooting_ = Switch, Preserve the rooting of rooted trees (default=0)