--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) |
