ml_phylogeny

--bootstrap-replications  
Integer: 1 <= x <= 1000 Number of times to resample data (default: 100)
-d, --destination <ClcServerObjectUrl> Destination file or folder on server. If not specified the folder of the first input object will be used.
--estimate-gamma <Boolean> Use expectation maximization to optimize gamma parameter (default: false)
--estimate-parameters <Boolean> Use expectation maximization to optimze rate substitution parameters. Note: Branch lengths are always optimized (default: true)
--estimate-topology <Boolean> Find maximum likelihood tree using tree swapping (topology changes) (default: true)
--gamma-parameter  
Double: 0.0 < x <= 1000.0 The parameter defining Gamma distribution (default: 1.0)
-i, --input <ClcObjectUrl> Input data on server
--include-rate-variation <Boolean> Include rate variation in likelihood calculations (default: false)
--log <Boolean> Enable creation of algo log file. (default: true)
--number-categories <[FOUR, EIGHT]> The number of substitution rate categories (default: FOUR)
--perform-bootstrap-analysis <Boolean> Resample data to estimate confidence in the tree. Note: This significantly increases the running time of this tool (default: false)
--protein-substitution-model  
<[BF,DAYHOFF, JTT, WAG]> Bishop Friday: assumes equal transition rates as well as equal equilibrium frequencies for all amino acids. Dayhoff: uses the transition rates and equilibrium frequencies determined by Dayhoff'79 (those used to define the PAM matrices). JTT: uses the transition rates and equilibrium frequencies determined by Jones, Taylor and Thornton'92. WAG: uses the transition rates and equilibrium frequencies determined by Whelan and Goldman'01. (default: WAG)
--ratio  
Double: 0.0 < x <= 1000.0 The ratio of the transition rate and the transversion rate (default: 2.0)
--starting-tree <ClcObjectUrl> Tree to use as the starting tree. This tree must have the same sequences as the input
--starting-tree-algo  
<[NEIGHBOR_JOINING, UPGMA]> Algorithm used to obtain a starting tree. UPGMA: Algorithm which assumes a constant rate of evolution. Neighbor Joining: Algorithm which does not assume a constant rate of evolution. (default: NEIGHBOR_JOINING)
--substitution-model  
<[JC, F81, K80,HKY, GTR]> Jukes Cantor: assumes equal transition rates as well as equal equilibrium frequencies for all bases. Felsenstein 81: assumes equal transition rates and equilibrium frequencies determined from the input sequence. Kimura 80: assumes equal equilibrium frequencies for all bases and has the transition/transversion ratio as a single parameter. HKY: assumes equilibrium frequencies determined from the input sequences and has the transition/transversion ratio as a single parameter. General Time Reversible: assumes equilibrium frequencies determined from the input sequences and has five substitution rate parameters. (default: JC)