-d, --destination <ClcServerObjectUrl> |
Destination file or folder on server. If not specified the folder of the first input object will be used. |
--do-aic <Boolean> |
Rank substitutional models based on minimum theoretical information criterion (AIC). Formula used is AIC = -2ln(L)+2K, where ln(L) is the loglikelihood of the best tree and K is number of parameters in the model. (default: true) |
--do-aicc <Boolean> |
Rank substitutional models based on minimum corrected theoretical information criterion (AICc). Formula used is AICc = -2ln(L)+2K + 2K(K+1)/(n-K-1), where ln(L) is the loglikelihood of the best tree, K is number of parameters in the model and n is length of the alignment. AICc is recommended over AIC roughly when n/K is less than 40. (default: true) |
--do-bic <Boolean> |
Rank substitutional models based on Bayesian information criterion (BIC). Formula used is BIC = -2ln(L)+Kln(n), where ln(L) is the loglikelihood of the best tree, K is number of parameters in the model and ln(n) is the logarithm of the length of the alignment. (default: true) |
--do-hlrt <Boolean> |
Perform hierarchical likelihood ratio tests (hLRT). (default: true) |
--hlrt-confidence |
|
Double: 1.0E-4 <= x <= 0.9999 |
Confidence level used in the likelihood ratio tests. (default: 0.01) |
-i, --input <ClcObjectUrl> |
Input data on server |
--log <Boolean> |
Enable creation of algo log file. (default: true) |
--starting-tree |
|
<[NEIGHBOR_JOINING,UPGMA]> |
Algorithm used to constuct a base tree. UPGMA: Algorithm which assumes a constant rate of evolution. Neighbor Joining: Algorithm which does not assume a constant rate of evolution. Topology of base tree is used in hLRT. Base tree is used as starting point for topology exploration in BIC, AIC and AICc ranking. (default: NEIGHBOR_JOINING) |
