Directory GDEHELP/HELP_WRITTEN/

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westram 2025-08-13 10:25 Rev.: 19532

* reintegrates 'help' into 'trunk'
- tweak arb documentation:
* automatically link
- ticket references to arb bug tracker (only affects html version).
- found URLs.
* page titles
- warn about long titles.
- introduce {{{SUBTITLE}}}s (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

6 lines of code changed in 5 files:

• GDEHELP/HELP_WRITTEN: MrBayes.help (+1 -1), ProbCons.help (+1 -1), fasttree.help (+1 -1), muscle.help (+1 -1), raxml8.help (+2 -2)

westram 2025-01-30 15:49 Rev.: 19501

* implements #865:
- allows to match species and table rows, using list entries (in cells and/or fields).

58 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: import_calc.help (+58 -4)

westram 2021-12-17 16:35 Rev.: 18865

* add minimal documentation for
- probcons and
- muscle.

29 lines of code changed in 2 files:

• GDEHELP/HELP_WRITTEN: ProbCons.help (new 16), muscle.help (new 13)

westram 2021-12-17 16:32 Rev.: 18863

* document 'Import fields from calc-sheet'.
* link to 'Export fields (to calc-sheet using NDS)'.
* add another pointer, where to add helpfiles for GDE menus.

42 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: import_calc.help (new 42)

westram 2021-11-10 15:36 Rev.: 18839

* upgrade {{{FastTree}}} to version 2.1.11
- cleanup: define flags and use make variables.
- specify fasttree version in help.
- update changelog.

5 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: fasttree.help (+5 -1)

westram 2021-11-07 20:29 Rev.: 18834

* use real LINK.

1 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: fasttree.help (+1 -1)

westram 2021-11-07 20:27 Rev.: 18833

* fix whitespace in HELP_WRITTEN.

46 lines of code changed in 5 files:

• GDEHELP/HELP_WRITTEN: MrBayes.help (+15 -15), MrBayesCustom.help (+16 -16), mafft.help (+8 -8), phyml-20130708.help (+4 -4), raxml.help (+3 -3)

westram 2021-11-07 20:25 Rev.: 18832

* improve documentation of generated help.

1 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: Readme (+1 -1)

westram 2021-11-04 16:54 Rev.: 18824

* add help for fasttree (copied start of text from homepage and link there).

24 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: fasttree.help (new 24)

westram 2017-10-27 16:33 Rev.: 16575

* mention raxml versions numbers (in help and menus)

3 lines of code changed in 2 files:

• GDEHELP/HELP_WRITTEN: raxml.help (+2), raxml8.help (+1)

westram 2016-12-17 13:12 Rev.: 15425

* reintegrates 'mladd' into 'trunk'
- improves raxml8 interface
* new functions
- score tree (=calculate likelihood and append to comment)
- calculate branchlengths
- optimize tree
- add to tree (implements #681)
* calculate bootstraps (as separate function or combined with other functions)
- allow to skip bootstrap calculation
* writes comment to generated trees (similar to raxml7-interface)
* fix key-wait on terminate
* time all functions
* fix thread usage
- use 'distinct alignment patterns' (as reported by RAxML) to select maximum threads
- slightly reduce threads in favor of asynchronous bootstrapping
- allow to override (used) cores and used threads separate
- adds {{{arb_write_tree_comment}}}
* adds: log:branches/mladd@15394,15396,15398:15424

89 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: raxml8.help (+89 -27)

westram 2016-12-05 17:03 Rev.: 15392

* reintegrates 'mladd' into 'trunk'
- adds help for RAxML8 integration (#623)
- remove default "non-random seed"
- fixes warnings about unrecommended use (messages where truncated; GTRGAMMA warning never showed up; GTRCAT warning always popped up)
- fixes CPU cores detection (broken by [14939])
* adds: log:branches/mladd@15377:15391

99 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: raxml8.help (new 99)

westram 2015-12-16 16:13 Rev.: 14622

* reintegrates 'ui' into 'trunk'
- implements #656
- adds instant update for
* next neighbour search
* branch analysis (mark functions)
* arb-phylo (filter setup)
* adds: log:branches/ui@14588:14621

2 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: MrBayes.help (+2 -2)

westram 2015-07-24 16:17 Rev.: 14080

* move sativa help template

15 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: sativa.help (new 15)

epruesse 2015-05-02 00:41 Rev.: 13797

fix spelling of likelihood

2 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: raxml.help (+2 -2)

westram 2014-07-17 11:25 Rev.: 12526

- remove broken help

0 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: raxml8.help (del)

epruesse 2014-07-16 23:26 Rev.: 12525

- add help for raxml8
- import normal tree also in quick mode
- check against too many/few sequences for model

0 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: raxml8.help (new)

westram 2013-10-18 14:22 Rev.: 10842

* reintegrates 'help' into 'trunk':
* adds:
- log:branches/help@10647:10841
- log:branches/helptest@10704:10720

4 lines of code changed in 2 files:

• GDEHELP/HELP_WRITTEN: MrBayesCustom.help (+1 -1), phyml-20130708.help (+3 -2)

westram 2013-09-17 15:07 Rev.: 10596

* fixed layout (of resulting html output)

42 lines of code changed in 3 files:

• GDEHELP/HELP_WRITTEN: MrBayes.help (+27 -17), MrBayesCustom.help (+2 -1), phyml-20130708.help (+13 -13)

aboeckma 2013-08-15 11:37 Rev.: 10455

Added !MrBayes custom command file menu

44 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: MrBayesCustom.help (new 44)

aboeckma 2013-08-15 10:12 Rev.: 10454

Added !MrBayes help

97 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: MrBayes.help (new 97)

aboeckma 2013-08-02 10:40 Rev.: 10403

minimalistic help file for mafft

81 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: mafft.help (new 81)

aboeckma 2013-07-23 13:21 Rev.: 10340

added phyml-20130708 help

160 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: phyml-20130708.help (new 160)

westram 2009-06-16 13:40 Rev.: 6064

- added RAxML bug to help

8 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: raxml.help (+8)

westram 2008-03-14 14:42 Rev.: 5255

- help for RAxML

162 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: raxml.help (new 162)

westram 2008-03-14 14:42 Rev.: 5254

- info about helpfiles here

7 lines of code changed in 1 file:

• GDEHELP/HELP_WRITTEN: Readme (new 7)