Author | Changes | Lines of Code | Lines per Change |
---|---|---|---|
Totals | 41 (100.0%) | 1095 (100.0%) | 26.7 |
epruesse | 25 (61.0%) | 598 (54.6%) | 23.9 |
westram | 16 (39.0%) | 497 (45.4%) | 31.0 |
* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19460:19479
6 lines of code changed in 1 file:
* 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:
* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19228:19233
13 lines of code changed in 3 files:
* avoid rule method fails, when no such directory exists.
1 lines of code changed in 1 file:
* 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:
* 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:
* 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:
* merge [15490] from 'warnings' into 'trunk'
- argument quoting for {{{arb_raxml8.sh}}}. thx to Elmar.
47 lines of code changed in 1 file:
* 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:
* 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:
* 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:
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:
update RAxML to 8.2.8
0 lines of code changed in 2 files:
* fix all broken mnemonics (missing, duplicates, wrong case)
* disable check in AWT_check_action_ids
2 lines of code changed in 1 file:
fix spelling of likelihood
1 lines of code changed in 1 file:
fix typo in makefile (should fix #612)
2 lines of code changed in 1 file:
fix AVX version not built due to "USE_GCC_46_OR_HIGHER" not exported
1 lines of code changed in 1 file:
remove double press-any-key
0 lines of code changed in 1 file:
- 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:
fix missing LD_LIBRARY_PATH setup
23 lines of code changed in 1 file:
first working version of RAxML8 integration
170 lines of code changed in 3 files:
- 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:
only build AVX version of RAxML if GCC >= 4.6.0
13 lines of code changed in 1 file:
try arb_sed instead of sed (uses gsed on osx)
1 lines of code changed in 1 file:
use suffix stamp for stamp files (ignored by arb_srclst.pl)
5 lines of code changed in 1 file:
fix OSX sed needs '' after -i
3 lines of code changed in 1 file:
initial add of RAxML 8
180 lines of code changed in 4 files: