TreeFix Change Log ----------------------- treefix-1.1.10 (2014/06/19) ----------------------- -- update libraries treefix-1.1.9 (2014/04/15) ----------------------- -- use one-sided SH test in raxmlmodel treefix-1.1.8 (2013/11/05) ----------------------- -- 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) ----------------------- - simplify version control treefix-1.1.6 (2012/11/06) ----------------------- - 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) ----------------------- - add TreeFix-RAxML to package treefix-1.1.4 (2012/08/17) ----------------------- - update raxmlmodel to use treefix_raxml namespace - fix setup.py script treefix-1.1.3 (2012/06/26) ----------------------- - 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) ----------------------- - 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) ----------------------- - 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) ----------------------- - 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) ----------------------- - initial release with TreeFix paper