New Features:

1. Alignment Maps

   Data support.

2. Likelihood computation using estimator for both TAB08 & KSA00 models
3. Map reconstruction using SA for both TAB08 & KSA00Maximum Likelihood Estimation (MLE)
4. Modify existing data set and create new data set.

Jobs Added:

Feature Details:

Alignment Maps

1. Multiple maps can be added by editing the model .xml file.

2. Cross counts are reported in the output window.

Likelihood using Estimator

Likelihood is computed for the data at the estimated model (from the same data).

Data support

Jobs can select data from a drop-down combo box. Only relevant data sets are shown. The application is preloaded with data sets.

Maximum Likelihood Estimation (MLE)

1. For Infinite-Alleles Model.

2. For Infinite-Sites Model

Data Set

Modify existing data set and create new data set.

1. When a job is run, the URL of the data set is given in the output window

2. Use Favorites to add the folder/file. Edit the data set and run jobs using the 

   drop-down data combo box.

3. Create a copy of the data set in the Favorites window; restart application to 

   see the data in the drop-down data combo box.

Simulated Annealing

Simulated Annealing (SA) for both genetic (TAB08) and physical (KSA00) model.

1. Turn on/off the log

2. Cross-counts (between start & best orders) in the output window.