TreeFix Change Log
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treefix-1.1.6 (2012/11/06)
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- changed treefix_raxml to use approximation for normal distribution if scipy library is not found
- updated README and examples to show how to pass parameters to likelihood/reconciliation modules


treefix-1.1.5 (2012/08/27)
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- added TreeFix-RAxML to package 


treefix-1.1.4 (2012/08/17)
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- updated raxmlmodel to use treefix_raxml namespace
- fixed setup.py script


treefix-1.1.3 (2012/06/26)
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- added versions to models
- fixed minor error in raxmlmodel not passing --eps
- moved processing of --extra parameter in models to constructor (from optimize_model)
- added change log to package


treefix-1.1.2 (2012/05/11)
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- moved check congruent gene tree to pre-processing step in search (affects bootstraps)
- added trivial bootstraps and fixed minor bug in output for special cases of small tree and input gene tree


treefix-1.1.1 (2012/05/08)
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- fixed major bug in p-value computation of previous release
- added pre-processing step to check input gene tree


treefix-1.1 (2012/03/26)
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- THIS VERSION INCLUDES A MAJOR BUG AND SHOULD NOT BE USED!
- added bootstrap analysis
- removed caching
- added pre-processing step to check congruent gene tree
- refactored code for computing likelihoods and costs into reuseable modules
- updated to use RAxML wrapper version 0.2


treefix-1.0 (2011/11/12)
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- initial release with TreeFix paper

