| 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 the 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 a name for the newly created concatenated alignment in the field |
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| 21 | "New alignment name". |
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| 22 | |
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| 23 | Use "Sequence Type" button to display the desired type of alignments/sequences |
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| 24 | from the database. |
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| 25 | |
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| 26 | Use Arrow buttons (located in between the lists) to select or remove the |
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| 27 | alignments into/from the "Alignments to be concatenated" list. |
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| 28 | |
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| 29 | You can also rearrange the order of concatenation of alignments by using "up" |
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| 30 | and "down" arrow keys (located by the side of "Alignments to be concatenated" |
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| 31 | list) before performing the actual concatenation. |
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| 32 | |
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| 33 | Pressing CLEAR LIST button clears the alignments list selected for |
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| 34 | concatenation. |
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| 35 | |
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| 36 | Use "Alignment Separator" to specify the tag/separator to be inserted into the |
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| 37 | target sequence data between the data of the alignments to be concatenated. |
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| 38 | |
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| 39 | Pressing the "CONCATENATE" button performs a concatenation of the alignments |
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| 40 | selected in the order given in the "Alignments to be concatenated" list. |
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| 41 | |
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| 42 | Use the "MERGE SIMILAR SPECIES" button to create new species by merging similar |
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| 43 | species (for e.g., similar species having different sequence alignments). |
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| 44 | This function is also available from the Species menu. |
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| 45 | See LINK{merge_species.hlp} for details. |
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| 46 | |
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| 47 | If the database contains similar species with different sequence alignments |
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| 48 | use "MERGE & CONCATENATE" button to generate new species by merging similar |
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| 49 | species in the database and concatenating the different sequence alignments |
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| 50 | contained in the newly merged species. |
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| 51 | |
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| 52 | NOTES |
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| 53 | |
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| 54 | If problems occurs during "Merging similar species" and/or "Concatenation", |
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| 55 | try the following - |
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| 56 | |
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| 57 | 1. Search the database for the "merged_species" field and mark the listed |
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| 58 | species, if any, and delete them. |
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| 59 | |
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| 60 | 2. Then search the database for the <criterion_field> to use for merging |
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| 61 | similar species. Mark the resulting species and perform merging similar |
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| 62 | species. |
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| 63 | |
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| 64 | 3. Usually newly generated (merged) species are marked and use the same to |
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| 65 | perform concatenation. CAUTION: Make sure that the new alignment name DOES NOT |
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| 66 | coinside with the selected alignments (names) to be concatenated! |
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| 67 | |
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| 68 | EXAMPLES See LINK{gene_species.hlp} |
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| 69 | |
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| 70 | WARNINGS None |
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| 71 | |
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| 72 | BUGS No bugs known |
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to organisms"
