| 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 | #************* Title of helpfile !! and start of real helpfile ******** |
|---|
| 11 | TITLE Concatenation of alignments/sequences |
|---|
| 12 | |
|---|
| 13 | DESCRIPTION |
|---|
| 14 | |
|---|
| 15 | With the help of the concatenation function, one can concatenate the aligned |
|---|
| 16 | sequences, which are contained in the same species preserving the ALIGNMENT. |
|---|
| 17 | Before using concatenation function make sure that the species contains more |
|---|
| 18 | than two aligned or unaligned sequences. |
|---|
| 19 | |
|---|
| 20 | Specify a name for the newly created concatenated alignment in the field |
|---|
| 21 | "New alignment name". |
|---|
| 22 | |
|---|
| 23 | Use "Sequence Type" button to display the desired type of alignments/sequences |
|---|
| 24 | from the database. |
|---|
| 25 | |
|---|
| 26 | Use Arrow buttons (located in between the lists) to select or remove the |
|---|
| 27 | alignments into/from the "Alignments to be concatenated" list. |
|---|
| 28 | |
|---|
| 29 | You can also rearrange the order of concatenation of alignments by using "up" |
|---|
| 30 | and "down" arrow keys (located by the side of "Alignments to be concatenated" |
|---|
| 31 | list) before performing the actual concatenation. |
|---|
| 32 | |
|---|
| 33 | Pressing CLEAR LIST button clears the alignments list selected for |
|---|
| 34 | concatenation. |
|---|
| 35 | |
|---|
| 36 | Use "Alignment Separator" to specify the tag/separator to be inserted into the |
|---|
| 37 | target sequence data between the data of the alignments to be concatenated. |
|---|
| 38 | |
|---|
| 39 | Pressing the "CONCATENATE" button performs a concatenation of the alignments |
|---|
| 40 | selected in the order given in the "Alignments to be concatenated" list. |
|---|
| 41 | |
|---|
| 42 | Use the "MERGE SIMILAR SPECIES" button to create new species by merging similar |
|---|
| 43 | species (for e.g., similar species having different sequence alignments). |
|---|
| 44 | This function is also available from the Species menu. |
|---|
| 45 | See LINK{merge_species.hlp} for details. |
|---|
| 46 | |
|---|
| 47 | If the database contains similar species with different sequence alignments |
|---|
| 48 | use "MERGE & CONCATENATE" button to generate new species by merging similar |
|---|
| 49 | species in the database and concatenating the different sequence alignments |
|---|
| 50 | contained in the newly merged species. |
|---|
| 51 | |
|---|
| 52 | NOTES |
|---|
| 53 | |
|---|
| 54 | If problems occurs during "Merging similar species" and/or "Concatenation", |
|---|
| 55 | try the following - |
|---|
| 56 | |
|---|
| 57 | 1. Search the database for the "merged_species" field and mark the listed |
|---|
| 58 | species, if any, and delete them. |
|---|
| 59 | |
|---|
| 60 | 2. Then search the database for the <criterion_field> to use for merging |
|---|
| 61 | similar species. Mark the resulting species and perform merging similar |
|---|
| 62 | species. |
|---|
| 63 | |
|---|
| 64 | 3. Usually newly generated (merged) species are marked and use the same to |
|---|
| 65 | perform concatenation. CAUTION: Make sure that the new alignment name DOES NOT |
|---|
| 66 | coinside with the selected alignments (names) to be concatenated! |
|---|
| 67 | |
|---|
| 68 | EXAMPLES See LINK{gene_species.hlp} |
|---|
| 69 | |
|---|
| 70 | WARNINGS None |
|---|
| 71 | |
|---|
| 72 | BUGS No bugs known |
|---|
