| 1 | #Please insert up references in the next lines (line starts with keyword UP) |
|---|
| 2 | UP arb.hlp |
|---|
| 3 | UP glossary.hlp |
|---|
| 4 | |
|---|
| 5 | #Please insert subtopic references (line starts with keyword SUB) |
|---|
| 6 | #SUB subtopic.hlp |
|---|
| 7 | |
|---|
| 8 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
|---|
| 9 | |
|---|
| 10 | |
|---|
| 11 | TITLE Column Statistic (Prototype) |
|---|
| 12 | |
|---|
| 13 | OCCURRENCE ARB EDITOR |
|---|
| 14 | |
|---|
| 15 | DESCRIPTION Highlites unlikely bases in an alignment using the maximum |
|---|
| 16 | likelihood technique. |
|---|
| 17 | As soon as the go button is pressed, the selected tree (by |
|---|
| 18 | ARB_NT) and all marked sequences are read. Then the relative |
|---|
| 19 | likelihood for each base is calculated and transformed to |
|---|
| 20 | a number between 0 and 9. This number is translated into a color, |
|---|
| 21 | using the colors 'RANGE 0 ... RANGE 9'. The higher the number, |
|---|
| 22 | the more unlikely a particular base. |
|---|
| 23 | You may improve the output by selecting a valid column statistic, |
|---|
| 24 | which holds information about column dependent rates and base |
|---|
| 25 | frequencies. |
|---|
| 26 | |
|---|
| 27 | NOTES The colors are not set correctly. Please set different 'CS' colors |
|---|
| 28 | <Props:Sequences: Colors and Fonts> and save them. |
|---|
| 29 | Without a powerfull computer only a small number of sequences can |
|---|
| 30 | be viewed. |
|---|
| 31 | The program assumes that your tree is correct. |
|---|
| 32 | |
|---|
| 33 | WARNINGS This is only a prototype, don't expect something perfect. |
|---|
| 34 | All sequences which should be analyzed should be marked and |
|---|
| 35 | in the tree shown by ARB_NT !!!!! |
|---|
| 36 | |
|---|
| 37 | BUGS The colors are not set correctly by default. |
|---|
| 38 | The program can only be started once. |
|---|
| 39 | |
|---|
| 40 | SECTION Detailed column statistic |
|---|
| 41 | |
|---|
| 42 | This special mode displays 4 rows below the sequence containing |
|---|
| 43 | the likelihood of each base character. |
|---|
| 44 | |
|---|
| 45 | Each row consists of two rows of digits displayed in the same color |
|---|
| 46 | (which actually is the color normally used for displaying the |
|---|
| 47 | appropriate base character). The upper of these two rows is the |
|---|
| 48 | first, the lower the second digit of the likelihood. |
|---|
| 49 | [You may like to use the cursor to simplify reading] |
|---|
| 50 | |
|---|
| 51 | Special character used: |
|---|
| 52 | ----------------------- |
|---|
| 53 | SPACE = likelihood is 20% |
|---|
| 54 | ^ = likelihood is 100% |
|---|
| 55 | ? = can't determine likelihood for that column |
|---|
| 56 | |
|---|
| 57 | Background colors used: |
|---|
| 58 | ----------------------- |
|---|
| 59 | Normally the normal background color is used. |
|---|
| 60 | |
|---|
| 61 | If a column has a significant likelihood for one base character |
|---|
| 62 | (or for the sum of two base characters), all four rows are |
|---|
| 63 | displayed in color 'Range 0'. |
|---|
| 64 | |
|---|
| 65 | [significance is 90% (hardcoded) - will be made utilizable soon] |
|---|
| 66 | |
|---|
| 67 | The single (or two) base character(s) responsive for the |
|---|
| 68 | significance will be displayed in colors 'Range 1' to 'Range 8' |
|---|
| 69 | (the higher the Range-number is, the higher is the likelihood) |
|---|
