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documentation updates docs #140: Commit 4760991 pushed by SebPorras
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Merge pull request #19 from bodenlab/dev docs #139: Commit 6b87849 pushed by SebPorras
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use gamma dist for col rates with mean 1 docs #138: Commit 060a100 pushed by SebPorras
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Merge pull request #18 from bodenlab/simple_dist docs #137: Commit e7fabc6 pushed by SebPorras
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remove IWD calc on known nodes, add complete TreeGazer tutorial docs #136: Commit 4926ea4 pushed by SebPorras
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handle internal data when -internal not specified, update docs docs #135: Commit fd51cee pushed by SebPorras
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Merge remote-tracking branch 'refs/remotes/origin/main' docs #134: Commit 4c3b368 pushed by SebPorras
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fixes null pointer exception in fitDistances(), j1 somtimes has no un… docs #133: Commit 0abc7fc pushed by SebPorras
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normalisation of distance penalties to improve MIP solutions docs #132: Commit 036654b pushed by SebPorras
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bug fix - inverse of branch length for penalty should be used docs #131: Commit 9776cd7 pushed by SebPorras
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update indel rates for pfam and uniref30 training alns, increase max … docs #130: Commit a6b26ee pushed by SebPorras
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update help info, change SCIP default params docs #129: Commit f73800a pushed by SebPorras
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indel solution fasta writer docs #128: Commit cb75e85 pushed by SebPorras
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change Gurobi parameters to defaults docs #127: Commit fe09507 pushed by SebPorras
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some bug fixes to TrAVIS command line, updates to match latest indel … docs #126: Commit 1240dc8 pushed by SebPorras
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Merge pull request #17 from bodenlab/mip_optimised docs #125: Commit 9025f10 pushed by SebPorras
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adds options to control TreeGazer ITOL output legend colour range docs #124: Commit 9bf3e25 pushed by SebPorras
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increase tolerence for empirical freqs docs #123: Commit e5452ea pushed by SebPorras
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mislabelled variable docs #122: Commit 3ca223f pushed by SebPorras
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remove magic numbers, fix header output bug docs #121: Commit 0122acd pushed by SebPorras
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handles runtime exceptions more elegantly, makes tied variances defau… docs #120: Commit f87c62e pushed by SebPorras
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major refactor of TreeGazer, formerly AnnotAceR docs #119: Commit 20fcd1e pushed by SebPorras
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update version date docs #118: Commit 8365f23 pushed by SebPorras
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adds empirical freq normalisation + removes CP-SAT option docs #117: Commit 376bb04 pushed by SebPorras
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add option for empirical frequencies for SubstModels. Updates TSVFile… docs #116: Commit 65e2964 pushed by SebPorras
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