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 CONCATENATION of ALIGNMENTS / SEQUENCES |
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12 | |
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13 | DESCRIPTION |
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14 | |
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15 | With the help of concatenation function, one can concatenate the aligned |
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16 | sequences, which are contained in the same species preserving the ALIGNMENT. |
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17 | Before using concatenation function make sure that the species contains more |
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18 | than two aligned or unaligned sequences. |
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19 | |
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20 | Specify new name for the newly created concatenated alignment in the field |
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21 | "New Alignment Name" (Make sure that the new alignment name starts with |
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22 | "ali_....."). |
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23 | |
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24 | Use "Sequence Type" button to load the desired type of alignments/sequences |
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25 | from the database. |
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26 | |
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27 | Use Arrow buttons (located in between the lists) to select or remove the |
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28 | alignments into/from the "Alignments to be concatenated" list. |
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29 | |
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30 | You can also rearrange the order of concatenation of alignments by using "up" |
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31 | and "down" arrow keys (located by the side of "Alignments to be concatenated" |
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32 | list) before performing actual concatenation. |
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33 | |
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34 | Pressing CLEAR LIST button clears the alignments list selected for |
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35 | concatenation. |
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36 | |
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37 | Use "Alignment Separator" to specify the tag/separator between the alignments |
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38 | to be concatenated. |
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39 | |
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40 | Pressing CONCATENATE button performs concatenation function for the alignments |
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41 | selected in the order of the alignments present in the "Alignments to be |
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42 | concatenated" list. |
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43 | |
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44 | Use MERGE SIMILAR SPECIES button to create new species by merging similar |
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45 | species (for e.g., Similar species having different sequence alignments). |
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46 | Additionally, you can do the same from the "Species" menu clicking on "Merge |
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47 | Similar Species" item. |
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48 | |
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49 | If the database contains similar species with different sequence alignments |
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50 | use "MERGE and CONCATENATE" button to generate new species by merging similar |
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51 | species in the database and concatenating the different sequence alignments |
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52 | contained in the newly merged species. |
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53 | |
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54 | NOTES |
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55 | |
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56 | If problems occurs during "Merging similar species" and/or "Concatenation", |
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57 | try the following - |
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58 | |
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59 | 1. Search the database for the "merged_species" field and mark the listed |
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60 | species, if any, and delete them. |
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61 | |
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62 | 2. Then search the database for the <criterion_field> to use for merging |
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63 | similar species. Mark the resulting species and perform merging similar |
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64 | species. |
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65 | |
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66 | 3. Usually newly generated (merged) species are marked and use the same to |
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67 | perform concatenation. CAUTION: Make sure that the new alignment name DOES NOT |
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68 | coinside with the selected alignments (names) to be concatenated !!! |
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69 | |
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70 | EXAMPLES None |
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71 | |
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72 | WARNINGS None |
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73 | |
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74 | BUGS No bugs known |
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