| 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 | |
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| 11 | TITLE Column Statistic (Prototype) |
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| 12 | |
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| 13 | OCCURRENCE ARB_EDIT4/View/Activate column statistics |
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| 14 | ARB_EDIT4/View/Disable column statistics |
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| 15 | ARB_EDIT4/View/Toggle detailed Col.-Stat. |
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| 16 | ARB_EDIT4/View/Set threshold for D.c.s. |
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| 17 | |
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| 18 | DESCRIPTION Highlights unlikely bases in an alignment using the maximum |
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| 19 | likelihood technique. |
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| 20 | |
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| 21 | As soon as the go button is pressed, the tree selected in ARB_NT |
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| 22 | and all marked sequences are read. Then the relative |
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| 23 | likelihood for each base is calculated and transformed to |
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| 24 | a number between 0 and 9. This number is translated into a color, |
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| 25 | using the colors 'RANGE 0 ... RANGE 9'. The higher the number, |
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| 26 | the more unlikely a particular base. |
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| 27 | |
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| 28 | You may improve the output by selecting a valid column statistic, |
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| 29 | which holds information about column dependent rates and base |
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| 30 | frequencies. |
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| 31 | |
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| 32 | NOTES To change the colors used for column statistics, |
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| 33 | edit "RANGE 0" up to "RANGE 9" in LINK{color_props.hlp}. |
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| 34 | |
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| 35 | All sequences that should be analyzed, have to be marked and |
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| 36 | have to be members of the tree currently shown in the ARB main window! |
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| 37 | The program assumes that your tree has good quality - if it does |
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| 38 | not, results may be quite useless. |
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| 39 | |
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| 40 | See also LINK{e4_background_priority.hlp}. |
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| 41 | |
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| 42 | WARNINGS This is only a prototype, don't expect something perfect. |
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| 43 | |
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| 44 | Without a powerful computer only a small number of sequences can |
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| 45 | be viewed. |
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| 46 | |
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| 47 | BUGS The program can only be started once. |
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| 48 | |
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| 49 | SECTION Detailed column statistic |
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| 50 | |
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| 51 | This special mode displays 4 rows below the sequence containing |
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| 52 | the likelihood of each base character. |
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| 53 | |
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| 54 | Each row consists of two rows of digits displayed in the same color |
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| 55 | (which actually is the color normally used for displaying the |
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| 56 | appropriate base character). The upper of these two rows is the |
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| 57 | first, the lower the second digit of the likelihood. |
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| 58 | [You may like to use the cursor to simplify reading] |
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| 59 | |
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| 60 | Special character used: |
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| 61 | ----------------------- |
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| 62 | SPACE = likelihood is 20% |
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| 63 | ^ = likelihood is 100% |
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| 64 | ? = can't determine likelihood for that column |
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| 65 | |
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| 66 | Background colors used: |
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| 67 | ----------------------- |
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| 68 | Normally the normal background color is used. |
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| 69 | |
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| 70 | If a column has a significant likelihood for one base character |
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| 71 | (or for the sum of two base characters), all four rows are |
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| 72 | displayed in color 'Range 0'. |
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| 73 | |
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| 74 | [significance is 90% (hardcoded) - will be made utilizable soon] |
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| 75 | |
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| 76 | The single (or two) base character(s) responsive for the |
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| 77 | significance will be displayed in colors 'Range 1' to 'Range 8' |
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| 78 | (the higher the Range-number is, the higher is the likelihood) |
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