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 | |
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7 | # Hypertext links in helptext can be added like this: LINK{ref.hlp|http://add|bla@domain} |
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8 | |
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9 | #************* Title of helpfile !! and start of real helpfile ******** |
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10 | TITLE How is the consensus calculated? |
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11 | |
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12 | OCCURRENCE ARB_NT/SAI/Create SAI using../Consensus |
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13 | ARB_EDIT4/Properties/Consensus definition |
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14 | |
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15 | DESCRIPTION What to do with gaps? |
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16 | |
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17 | If a column contains only gaps the result will be shown as '='. |
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18 | |
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19 | Define whether to use or to ignore gaps entirely: |
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20 | |
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21 | If you count gaps and the gap frequency exceeds 'threshold for gaps', |
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22 | the result will be shown as '-'. |
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23 | |
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24 | If the switch is 'off', the algorithm will virtually remove all gaps. |
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25 | That means if you have a column with two 'A's |
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26 | and 500 gaps the program thinks of 100% 'A'. |
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27 | (If the switch is 'on', the relative number of 'A's would be 2%) |
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28 | |
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29 | Simplify using IUPAC |
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30 | |
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31 | Define whether the most frequent base or the IUPAC code |
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32 | (more then one base) should be shown at the particular |
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33 | position by pressing the respective checkbox after the |
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34 | 'simplify' prompt. |
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35 | |
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36 | Characters are used for IUPAC encoding only if their |
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37 | frequency exceeds 'threshold for character'. |
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38 | |
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39 | Example: |
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40 | |
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41 | If you have 40% 'A', 10% 'C', 40% 'G' and 10% 'T' and |
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42 | 'threshold for character' is set to 20%, the |
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43 | program looks for a iupac code only for 'A' and 'G'. |
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44 | |
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45 | Note: |
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46 | |
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47 | The IUPAC codes are displayed after pressing |
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48 | the 'show IUPAC' button. |
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49 | |
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50 | Show as upper or lower case? |
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51 | |
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52 | Define whether the character is displayed in upper or lower case |
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53 | or whether a dot is displayed. |
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54 | |
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55 | Define upper and lower limit: |
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56 | |
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57 | If the percentage of a character is above or equal to the upper |
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58 | limit, the character is displayed in upper case. |
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59 | |
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60 | If the percentage of a character is above or equal to the lower |
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61 | limit and below the upper limit, the character is displayed in lower case. |
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62 | |
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63 | Otherwise a dot ('.') is displayed. |
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64 | |
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65 | NOTES None |
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66 | |
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67 | EXAMPLES None |
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68 | |
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69 | WARNINGS IUPAC symbols in source sequences are ignored. |
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70 | |
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71 | BUGS 'LINK{consensus.ps}' is broken for more than 10 years |
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72 | now. Seems that nobody ever took a look. |
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73 | |
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