| 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 Alignment adaption (select species) |
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| 12 | |
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| 13 | Select species to use for alignment adaption |
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| 14 | |
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| 15 | OCCURRENCE ARB_MERGE/TRANSFER SPECIES (Adapt alignment/SELECT) |
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| 16 | |
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| 17 | DESCRIPTION Helps you finding candidates for alignment preservation. |
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| 18 | |
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| 19 | Normally people have inserted new gaps in one of the two databases. |
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| 20 | ARB Merge tries to adapt the alignment. |
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| 21 | |
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| 22 | To be able to do this, you have to specify one or more species or SAIs |
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| 23 | existing in BOTH databases. ARB Merge then creates a column reference list |
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| 24 | and realigns all transferred species according to this list. |
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| 25 | |
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| 26 | Press the 'Find candidates' button to search both databases for candidate |
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| 27 | species/SAIs and rate them. |
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| 28 | |
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| 29 | A list of species/SAIs shows up. The first column contains the name, |
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| 30 | the second column the number of alignments containing data for this species/SAI, |
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| 31 | the third column shows the position-count-difference (see below), |
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| 32 | the fourth column is the score (higher value means better). |
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| 33 | |
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| 34 | The list is sorted by score, i.e. best candidates are listed at the top. |
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| 35 | |
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| 36 | The term 'position-count-difference' is calculated like follows: |
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| 37 | For all alignments the number of non-gaps (i.e. neither '-' nor '.') are counted and |
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| 38 | the differences between these counts are summarized for all alignments. |
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| 39 | Best value is 0, which normally means the sequence data of the species (or the SAI data) |
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| 40 | didn't change. A high value means that species changed data and isn't a good candidate |
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| 41 | for alignment preservation. |
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| 42 | |
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| 43 | To enable this feature, enable the 'Adapt alignment' toggle. |
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| 44 | |
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| 45 | NOTES In our database releases we provide SAIs named 'gaps_...'. |
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| 46 | These SAIs are the best candidates for alignment preservation. |
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| 47 | |
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| 48 | When merging similar databases with many species, searching adapt candidates |
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| 49 | may take a long time. Press KILL in the status window to abort the process. |
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| 50 | |
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| 51 | EXAMPLES None |
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| 52 | |
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| 53 | WARNINGS Calculated SAIs (like MAX_FREQUENCY or POS_VAR_BY_PARSIMONY) show up on top |
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| 54 | but they are normally NO good candidates for preservation. |
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| 55 | |
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| 56 | BUGS No bugs known |
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