TreeFix Change Log
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treefix-1.1.10 (2014/06/19)
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-- update libraries


treefix-1.1.9 (2014/04/15)
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-- use one-sided SH test in raxmlmodel


treefix-1.1.8 (2013/11/05)
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-- add input checks (rooted, binary trees; matching alignment, gene tree, species tree, species map)
-- add --maxtime parameter for search
-- add tree-annotate script for event/homolog inference


treefix-1.1.7 (2012/12/14)
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- simplify version control


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


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


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


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


treefix-1.1.2 (2012/05/11)
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- move check congruent gene tree to pre-processing step in search (affects bootstraps)
- add 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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- fix major bug in p-value computation of previous release
- add 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!
- add bootstrap analysis
- remove caching
- add pre-processing step to check congruent gene tree
- refactor code for computing likelihoods and costs into reuseable modules
- update to use RAxML wrapper version 0.2


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

