| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | |
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| 5 | #Please insert subtopic references (line starts with keyword SUB) |
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| 6 | #SUB subtopic.hlp |
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| 7 | |
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| 8 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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| 9 | |
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| 10 | #************* Title of helpfile !! and start of real helpfile ******** |
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| 11 | TITLE Mark long branches |
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| 12 | |
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| 13 | OCCURRENCE ARB_NT |
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| 14 | |
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| 15 | DESCRIPTION Badly aligned sequences often result in long branches in the |
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| 16 | tree. Being able to identify those branches quickly helps to |
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| 17 | find those sequences. |
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| 18 | |
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| 19 | The programs allows to mark all species having an extra |
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| 20 | long branch compared with it's neighbour branch. |
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| 21 | |
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| 22 | Enter two values separated by comma into the input field: |
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| 23 | * first the minimum relative difference between two neighbour |
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| 24 | branches you want to have marked. |
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| 25 | |
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| 26 | Examples: |
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| 27 | |
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| 28 | 100 = mark branches that have more than the double length |
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| 29 | compared with their neighbour branch |
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| 30 | 10 = mark branches that are more than 10% longer |
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| 31 | 0 = mark branches that are longer than their neighbour branch |
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| 32 | |
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| 33 | * second the minimun absolute difference between two neighbour |
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| 34 | branches. The unit is the same as used in branchlength. |
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| 35 | |
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| 36 | NOTES If a branch was marked - it's parent branches will not be marked, |
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| 37 | i.e. the function does not mark ALL extra long branches, only those |
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| 38 | nearest to the tips of the trees will get marked - otherwise the |
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| 39 | output won't be useful. |
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| 40 | |
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| 41 | Intended workflow is: |
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| 42 | * Search long branches |
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| 43 | * Check alignment and data and maybe fix it |
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| 44 | * Recalculate tree parts (see LINK{pa_add.hlp}) |
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| 45 | * Search again. Now you most likely will find other branches. |
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| 46 | |
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| 47 | EXAMPLES None |
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| 48 | |
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| 49 | WARNINGS None |
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| 50 | |
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| 51 | BUGS No bugs known |
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