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Last change
on this file was
19532,
checked in by westram, 4 months ago
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- reintegrates 'help' into 'trunk'
- tweak arb documentation:
- automatically link
- ticket references to arb
 tracker (only affects html version).
- found URLs.
- page titles
- warn about long titles.
- introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
- increase allowed length (limited by subwindow width).
- cleanup header sections in all helpfiles.
- fix and/or update several help files.
- document syntax of help sources.
- build issues:
- when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
- remove output files on error (including files below ARBHOME/lib).
- pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
- moves Tree admin + NDS menu entries to top of menu
- adds: log:branches/help@18783:19531
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Property svn:eol-style set to
native
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Property svn:keywords set to
Author Date Id Revision
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File size:
1.5 KB
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| 1 | # main topics: |
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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 | # sub topics: |
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| 6 | #SUB subtopic.hlp |
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| 7 | |
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| 8 | # format described in ../help.readme |
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| 9 | |
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| 10 | |
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| 11 | TITLE Partial sequences |
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| 12 | |
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| 13 | OCCURRENCE General |
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| 14 | |
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| 15 | DESCRIPTION Species should contain an entry 'ARB_partial' specifying |
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| 16 | whether the associated sequence is a "full sequence" or |
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| 17 | a "partial sequence". |
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| 18 | |
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| 19 | If 'ARB_partial' is 1 then the sequence is considered partial. |
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| 20 | |
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| 21 | There's a special function to add partial sequences |
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| 22 | (see LINK{pa_partial.hlp}). |
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| 23 | |
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| 24 | NOTES There are several function to find and mark species with |
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| 25 | partial or full sequence in the Species menu. |
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| 26 | |
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| 27 | EXAMPLES Attraction of partial sequences (when added as full sequence): |
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| 28 | |
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| 29 | Species1 .....NNNNNNNNNNN............................. |
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| 30 | Species2 .......................NNNNNNNNNNNNNN........ |
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| 31 | |
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| 32 | The calculated distance between 'Species1' and 'Species2' will be ZERO |
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| 33 | when they are added as full sequences and as a result they will group |
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| 34 | together. |
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| 35 | |
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| 36 | Adding them as partial sequences will avoid that problem. |
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| 37 | |
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| 38 | WARNINGS Partial sequences cannot be used to calculate trees. Currently |
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| 39 | this isn't forbidden, but it's highly recommended not to do that. |
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| 40 | |
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| 41 | Instead remove all species with partial sequences from the tree, |
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| 42 | then optimize the tree and afterwards add the removed species again |
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| 43 | using LINK{pa_partial.hlp}. |
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| 44 | |
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| 45 | BUGS No bugs known |
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