Directory GDE/RAxML8/

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Most Recent Commits

westram 2023-08-11 13:40 Rev.: 19480

* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19460:19479

6 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+6 -5)

westram 2022-09-01 16:19 Rev.: 19245

* reintegrates 'sina' into 'trunk'
- build/deliver sina together with arb
* adds: log:branches/sina@18984:19043,19046:19069,19072:19244

8 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+8 -2)

westram 2022-08-12 18:40 Rev.: 19234

* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19228:19233

13 lines of code changed in 3 files:

• GDE/RAxML8: Makefile (+3 -1), arb_raxml8.sh (+10 -29), raxml8.menu (del)

westram 2022-03-04 16:11 Rev.: 18961

* avoid rule method fails, when no such directory exists.

1 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+1 -1)

westram 2019-10-03 10:08 Rev.: 18140

* full update from child 'fix' into 'trunk'
- improve target 'cleanRelinkable'
- fix crash in inotify file tracker (occurred when moving a tracked file)
- minor tweaks for fts
* adds: log:branches/fix@18131:18139

4 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+4)

westram 2019-09-26 18:39 Rev.: 18120

* add new target 'cleanRelinkable':
- removes libs, executables + tests to reduce size of WC (esp. in sanitized builds).
- avoid 'cleanRelinkable' causes rebuild (esp. rebuild of RaxML8).
* fix bogus-error when target 'clean' in UNIT_TESTER got called.

4 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+4 -4)

westram 2019-03-04 15:22 Rev.: 17634

* reintegrates 'mix' into 'trunk'
* prepare arb for hybrid svn/git use (central svn + local git)
* adds: log:branches/mix@17631:17633

3 lines of code changed in 1 file:

• GDE/RAxML8: .gitignore (new 3)

westram 2017-01-02 12:40 Rev.: 15491

* merge [15490] from 'warnings' into 'trunk'
- argument quoting for {{{arb_raxml8.sh}}}. thx to Elmar.

47 lines of code changed in 1 file:

• GDE/RAxML8: arb_raxml8.sh (+47 -47)

westram 2016-12-30 13:05 Rev.: 15482

* partial merge from 'warnings' into 'trunk'
- fixes for {{{arb_raxml8.sh}}}
* OSX compatibility (grep/sed)
* {{{LD_LIBRARY_PATH}}}
* adds: log:branches/warnings@15476,15478

10 lines of code changed in 1 file:

• GDE/RAxML8: arb_raxml8.sh (+10 -4)

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

339 lines of code changed in 2 files:

• GDE/RAxML8: arb_raxml8.sh (+310 -80), raxml8.menu (+29 -14)

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

60 lines of code changed in 2 files:

• GDE/RAxML8: arb_raxml8.sh (+43 -29), raxml8.menu (+17 -18)

epruesse 2016-06-14 20:17 Rev.: 14939

update RAxML8 GDE gui + script
- silence grep and which (printed to stderr as side effect)
- detect cpu core limit for Torque/PBS jobs
- make building and importing the MRE tree optional
- allow giving the tree a name (rather than default importing as tree_raxml)

53 lines of code changed in 2 files:

• GDE/RAxML8: arb_raxml8.sh (+41 -15), raxml8.menu (+12 -1)

epruesse 2016-06-14 20:00 Rev.: 14938

update RAxML to 8.2.8

0 lines of code changed in 2 files:

• GDE/RAxML8: standard-RAxML-8.0.26.tar.gz (del), standard-RAxML-8.2.8.tar.gz (new)

westram 2016-05-19 14:06 Rev.: 14852

* fix all broken mnemonics (missing, duplicates, wrong case)
* disable check in AWT_check_action_ids

2 lines of code changed in 1 file:

• GDE/RAxML8: raxml8.menu (+2 -1)

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

fix spelling of likelihood

1 lines of code changed in 1 file:

• GDE/RAxML8: raxml8.menu (+1 -1)

epruesse 2014-10-07 12:44 Rev.: 12994

fix typo in makefile (should fix #612)

2 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+2 -2)

epruesse 2014-07-18 14:50 Rev.: 12533

fix AVX version not built due to "USE_GCC_46_OR_HIGHER" not exported

1 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+1 -1)

epruesse 2014-07-18 12:43 Rev.: 12532

remove double press-any-key

0 lines of code changed in 1 file:

• GDE/RAxML8: arb_raxml8.sh (-1)

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

21 lines of code changed in 1 file:

• GDE/RAxML8: arb_raxml8.sh (+21 -6)

epruesse 2014-07-16 13:55 Rev.: 12523

fix missing LD_LIBRARY_PATH setup

23 lines of code changed in 1 file:

• GDE/RAxML8: arb_raxml8.sh (+23 -1)

epruesse 2014-07-16 02:36 Rev.: 12517

first working version of RAxML8 integration

170 lines of code changed in 3 files:

• GDE/RAxML8: Makefile (+2 -1), arb_raxml8.sh (+138 -39), raxml8.menu (+30 -2)

epruesse 2014-07-15 23:43 Rev.: 12514

- fix test case failing because of added menu item
(not sure about verifying the number of menu items in cxx unit tests...)
- fix arb_srclist.pl not knowning what to do with arb_raxml8
- some fixes to script (not yet working)

125 lines of code changed in 4 files:

• GDE/RAxML8: Makefile (+1 -1), arb_raxml8 (del), arb_raxml8.sh (new 117), raxml8.menu (+7 -7)

epruesse 2014-07-15 22:24 Rev.: 12513

only build AVX version of RAxML if GCC >= 4.6.0

13 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+13 -8)

epruesse 2014-07-15 20:45 Rev.: 12512

try arb_sed instead of sed (uses gsed on osx)

1 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+1 -3)

epruesse 2014-07-15 20:41 Rev.: 12510

use suffix stamp for stamp files (ignored by arb_srclst.pl)

5 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+5 -5)

epruesse 2014-07-15 20:24 Rev.: 12509

fix OSX sed needs '' after -i

3 lines of code changed in 1 file:

• GDE/RAxML8: Makefile (+3 -1)

epruesse 2014-07-15 17:25 Rev.: 12508

initial add of RAxML 8

180 lines of code changed in 4 files:

• GDE/RAxML8: Makefile (new 57), arb_raxml8 (new 72), raxml8.menu (new 50), standard-RAxML-8.0.26.tar.gz (new 1)