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New Features:
- Alignment Maps
- Likelihood computation using estimator for both TAB08 & KSA00 models
- Map reconstruction using SA for both TAB08 & KSA00.
Jobs Added:
Feature Details:
Alignment Maps
Multiple maps can be added by editing the model .xml file.
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).
Choice of estimators in a drop-down combo box
Data Set
Modify existing data set and create new data set.
When a job is run, the URL of the data set is given in the output window
Use Favorites to add the folder/file. Edit the data set and run jobs using the
drop-down data combo box.
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.
Turn on/off the log
Cross-counts (between start & best orders) in the output window.
Release Notes
Coalescent 1.4.0:
Bug
- [COALESCENT-24] - IllegalStateException in ExactRecursionListener
- [COALESCENT-29] - Genealogy Probability work-around Fixed
Design
- [COALESCENT-28] - Statistic.alleles() from Set to Iterable
Feature
- [COALESCENT-12] - Data support
- [COALESCENT-14] - Statistic: Allele based Iteration
- [COALESCENT-19] - Acceptance Test
- [COALESCENT-22] - Console application
- [COALESCENT-31] - MLE (Exact) of theta for K69
- [COALESCENT-40] - MLE (Exact) of theta for KC64
Refactor
- [COALESCENT-20] - Builder and Provider-Impls Updated
- [COALESCENT-27] - BigDecimal in Statistic
Task
- [COALESCENT-41] - GeneTree Test Updated
Commons 1.2.2:
Feature
- [COMMONS-61] - Likelihood with Estimators
- [COMMONS-62] - Compute Model Likelihood
- [COMMONS-63] - Model Estimation
- [COMMONS-67] - Key-Value Combo Builder Property
Task
- [COMMONS-53] - Model & Data Simulation Interface
- [COMMONS-64] - A StringList2 Provider: WHITE-SPACE
- [COMMONS-65] - A StringList Provider: WHITE-SPACE