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| 1 | Output of PhyML execution: |
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| 2 | - use monospace font |
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| 3 | - scroll down to follow the progress of the execution |
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| 4 | |
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| 5 | When GTR is on -> transition/transversion ratio option should be off. |
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| 6 | |
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| 7 | Suppress the black horizontal lines separating the sub-sections |
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| 8 | |
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| 9 | Replace PhyMLGuifiles/ by bin/ in PhyMLPanel.java |
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| 10 | |
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| 11 | |
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| 12 | Replace #Subcategories by # of rate classes |
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| 13 | |
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| 14 | Replace Gamma with Shape parameter and Alpha with Value |
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| 15 | |
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| 16 | Boxes and buttons seem to be a bit all over the place. Is it possible |
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| 17 | to justify them? For example, a starting point could be to set all |
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| 18 | the boxes to the same width, same of the scrolldown menus. |
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| 19 | |
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| 20 | Optimise Rate Parameter should be only active when the model |
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| 21 | selected is GTR. When model=custom it should be set to 'yes' |
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| 22 | with no option to change it. |
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