| 4881d83 | stamatak | 20 July 2016, 09:12:46 UTC | update readme | 20 July 2016, 09:12:46 UTC |
| e3641a5 | stamatak | 20 July 2016, 09:11:22 UTC | added flag: --print-identical-sequences that will tell RAxML to remove undetermined columns in the .reduced MSA file, but not remove identical sequences | 20 July 2016, 09:11:22 UTC |
| 462bf85 | stamatak | 19 July 2016, 07:43:10 UTC | adapted Dave Sowfford's fix for regularly flushing stdout to RAxML coding style | 19 July 2016, 07:43:10 UTC |
| a778395 | Alexis Stamatakis | 19 July 2016, 07:38:05 UTC | Merge pull request #38 from swofford/master periodically flush stdout by Dave Swofford | 19 July 2016, 07:38:05 UTC |
| 172e263 | Dave Swofford | 16 July 2016, 18:27:37 UTC | fix comment typo | 16 July 2016, 18:27:37 UTC |
| b12e229 | Dave Swofford | 16 July 2016, 18:11:13 UTC | periodically flush stdout | 16 July 2016, 18:11:13 UTC |
| 2a8fbd9 | stamatak | 14 July 2016, 06:42:02 UTC | added end of line to tree written to file be the -f I rooting option | 14 July 2016, 06:42:02 UTC |
| 3abe69b | Alexis Stamatakis | 19 April 2016, 06:34:16 UTC | Merge pull request #36 from hyphaltip/patch-1 Update axml.c | 19 April 2016, 06:34:16 UTC |
| d76ce5c | Jason Stajich | 19 April 2016, 06:32:37 UTC | Update axml.c typo in the docu: outgrpoup to outgroup | 19 April 2016, 06:32:37 UTC |
| a4782b3 | stamatak | 04 April 2016, 18:50:06 UTC | no changes | 04 April 2016, 18:50:06 UTC |
| 28aec8c | stamatak | 04 April 2016, 18:47:09 UTC | Merge branch 'master' of github.com:stamatak/standard-RAxML Conflicts: axml.c | 04 April 2016, 18:47:09 UTC |
| 76ace99 | stamatak | 04 April 2016, 18:38:30 UTC | changes? | 04 April 2016, 18:38:30 UTC |
| 8ce66e0 | Alexis Stamatakis | 04 April 2016, 18:34:23 UTC | Merge pull request #35 from algomaus/master Fixed numerical error for large number of taxa and added comments | 04 April 2016, 18:34:23 UTC |
| 4eabac0 | Sarah Lutteropp | 04 April 2016, 09:58:06 UTC | Added simple MPI version for sampling quartets without replacement | 04 April 2016, 09:58:06 UTC |
| 0bf918a | Sarah Lutteropp | 04 April 2016, 08:46:02 UTC | Merge remote-tracking branch 'upstream/master' Conflicts: axml.c | 04 April 2016, 08:46:02 UTC |
| 354dc87 | stamatak | 24 March 2016, 21:10:56 UTC | Merge branch 'master' of https://github.com/algomaus/standard-RAxML into algomaus-master Conflicts: axml.c | 24 March 2016, 21:10:56 UTC |
| 63375cd | Sarah Lutteropp | 24 March 2016, 20:02:42 UTC | added more comments to random quartet generation | 24 March 2016, 20:02:42 UTC |
| 1348273 | Sarah Lutteropp | 24 March 2016, 19:48:17 UTC | Added more comments to the random quartets code | 24 March 2016, 19:48:17 UTC |
| 2213a94 | Sarah Lutteropp | 24 March 2016, 18:59:04 UTC | Fixed numerical error in random quartets that happened if the number of taxa was greater than 1000. With the corrected version, random quartet generation works for up to 100000 taxa. | 24 March 2016, 18:59:04 UTC |
| 68c878e | stamatak | 23 March 2016, 09:49:50 UTC | updated manual | 23 March 2016, 09:49:50 UTC |
| 799fb9b | stamatak | 23 March 2016, 09:46:52 UTC | cosmetic change | 23 March 2016, 09:46:52 UTC |
| a3d3006 | stamatak | 23 March 2016, 09:41:50 UTC | integrated Sarah's code for randomly subsampling quartets without replacement. | 23 March 2016, 09:41:50 UTC |
| 0173e9f | Alexis Stamatakis | 23 March 2016, 09:07:25 UTC | Merge pull request #33 from algomaus/master Implemented faster quartet sampling algorithm | 23 March 2016, 09:07:25 UTC |
| da70866 | Sarah Lutteropp | 22 March 2016, 15:36:31 UTC | Implemented faster quartet sampling algorithm | 22 March 2016, 15:36:31 UTC |
| e85608c | stamatak | 22 March 2016, 14:40:49 UTC | added acknowledgement | 22 March 2016, 14:40:49 UTC |
| 2e9108d | stamatak | 22 March 2016, 14:37:00 UTC | added sarah's quartet sampling code | 22 March 2016, 14:37:00 UTC |
| 0deb8b7 | stamatak | 17 March 2016, 13:56:07 UTC | small cosmetic change | 17 March 2016, 13:56:07 UTC |
| b15029e | stamatak | 17 March 2016, 10:27:56 UTC | commented and cleaned up quartet calculation code for Sarah | 17 March 2016, 10:27:56 UTC |
| 76cf782 | stamatak | 17 March 2016, 08:25:42 UTC | added new windows executables by ingo michalak | 17 March 2016, 08:25:42 UTC |
| e303c46 | stamatak | 17 March 2016, 08:24:57 UTC | removed old 3rd part windows executables | 17 March 2016, 08:24:57 UTC |
| 05b227c | stamatak | 14 March 2016, 15:45:50 UTC | fixed failing assertion for randomized quartet subsampling via a pretty awful hack, while doing this it became evident that the specification for this is not totally clear | 14 March 2016, 15:45:50 UTC |
| 222e44a | Alexis Stamatakis | 11 March 2016, 08:16:40 UTC | Merge pull request #28 from hrabe/my-add-gitignore-file Add qualified .gitignore file | 11 March 2016, 08:16:40 UTC |
| 7a01b4e | Alexis Stamatakis | 11 March 2016, 08:15:47 UTC | Merge pull request #24 from hrabe/my-fix-timer-issue Fix negative time duration calculation/output on Windows builds | 11 March 2016, 08:15:47 UTC |
| a1e53bc | stamatak | 10 March 2016, 14:29:10 UTC | some native windows-compilation related fixes | 10 March 2016, 14:29:10 UTC |
| ce47ce6 | stamatak | 10 March 2016, 14:02:47 UTC | made tree parsing error reporting even more verbose | 10 March 2016, 14:02:47 UTC |
| acfd2ac | stamatak | 10 March 2016, 13:34:07 UTC | -added more verbose tree parser error messages for multi-furcating trees that will help to easily fix ill-formatted trees with excessive parentheses that look like this: r,((x,(y,z))),u and transform them into this: r,(x,(y,z)),u -added LG4X bug fix for the PThreads version -added option --bootstop-perms=number that allows for specifying the number of permutation replicates to carry out in the bootstrap convergence test. | 10 March 2016, 13:34:07 UTC |
| 28c61b9 | stamatak | 10 March 2016, 13:26:34 UTC | updated manual | 10 March 2016, 13:26:34 UTC |
| 3d8a81f | Heiko Rabe | 02 March 2016, 15:05:14 UTC | Restrict .gitignore to main folder only Would not permit to update already contained Windows binaries otherwise. | 02 March 2016, 15:05:14 UTC |
| 7d66873 | Heiko Rabe | 01 March 2016, 16:17:49 UTC | Add qualified .gitignore file Specifies intentionally untracked files to ignore See https://git-scm.com/docs/gitignore | 01 March 2016, 16:17:49 UTC |
| 8b9f07d | Heiko Rabe | 01 March 2016, 12:31:56 UTC | Fix negative time duration calculation/output on Windows builds This bug affects the time duration for bootstraps and total times. Example: one bootstrap started 16:59:00 and ends 17:01:00 -> wrong calculated as: 1*60 + 0 - 59*60 + 0 = -3480.0 seconds Solution: Windows equivalent for gettimeofday() has been implemented. | 01 March 2016, 12:31:56 UTC |
| f5d0d44 | stamatak | 26 February 2016, 21:21:21 UTC | 1. changed BS replicate generation option -f j to refuse generating BS replicates if original alignment contains completely undetermined columns 2. small fix in LG4X model param optimization that will hopefully solve the issues with LG4X | 26 February 2016, 21:21:21 UTC |
| 640b68a | stamatak | 24 February 2016, 07:18:28 UTC | updated BS replicate generation to also generate correct bootstrap partition files. | 24 February 2016, 07:18:28 UTC |
| 4692545 | stamatak | 02 February 2016, 16:04:47 UTC | added cross compiled windows executables | 02 February 2016, 16:04:47 UTC |
| 5ebeb78 | stamatak | 09 December 2015, 09:46:36 UTC | added version 8.2.4 windows executables | 09 December 2015, 09:46:36 UTC |
| d84251a | stamatak | 02 October 2015, 13:45:38 UTC | updated README and Release-Notes to show the correct version number | 02 October 2015, 13:45:38 UTC |
| 716bbc7 | stamatak | 02 October 2015, 13:41:21 UTC | updated on-line help and manual (--asc-miss flag was removed) | 02 October 2015, 13:41:21 UTC |
| 9ab50c4 | stamatak | 02 October 2015, 13:34:09 UTC | fixed two bugs: 1. bug with asc bias calculations using the pthreads version, the experimental missing data modeling option caused problems and was removed because it did not work anyway 2. added check such that memory saving -U is not used in conjunction with proportion of invar sites estimates for which it was never implemented | 02 October 2015, 13:34:09 UTC |
| 70c66a0 | stamatak | 12 August 2015, 07:47:19 UTC | 1. Integrated fallback for BFGS optimization to Brent-based optimization in case BFGS requires too many parameters. 2. Raised the minimum rate value to 0.0001 | 12 August 2015, 07:47:19 UTC |
| 4c26b88 | stamatak | 10 August 2015, 16:59:37 UTC | added modified makefiles that will do a clean build (i.e. remove all .o and the corresponding executable prior to compiling) to avoid frequent erroneous use and questions on the RAxML google group when users forgot to remove .o files prior to building a different binary. For development purposes this can be disabled by specifying the dev target | 10 August 2015, 16:59:37 UTC |
| a9b2aa2 | stamatak | 06 August 2015, 10:20:46 UTC | updated axml.h | 06 August 2015, 10:20:46 UTC |
| 5439677 | stamatak | 06 August 2015, 10:00:58 UTC | -changed optimization procedure for LG4X | 06 August 2015, 10:00:58 UTC |
| 09a8bf2 | stamatak | 05 August 2015, 16:55:16 UTC | added an assertion | 05 August 2015, 16:55:16 UTC |
| 0468ca3 | stamatak | 05 August 2015, 09:42:26 UTC | cleaned up the code | 05 August 2015, 09:42:26 UTC |
| 9a02452 | stamatak | 05 August 2015, 09:34:38 UTC | fixed numerical problem in BFGS optimization | 05 August 2015, 09:34:38 UTC |
| 4319e00 | stamatak | 10 July 2015, 07:47:50 UTC | updated windows binaries | 10 July 2015, 07:47:50 UTC |
| ea59703 | stamatak | 09 July 2015, 17:22:07 UTC | updated manual | 09 July 2015, 17:22:07 UTC |
| 8aeb9a9 | stamatak | 09 July 2015, 17:06:34 UTC | added Kassian's code for TC/IC score calculations on partial gene trees added HKY85 model added some experimental code | 09 July 2015, 17:06:34 UTC |
| ebd95ce | stamatak | 01 July 2015, 10:02:36 UTC | updated windows executables | 01 July 2015, 10:02:36 UTC |
| 852d2a5 | stamatak | 29 June 2015, 16:07:37 UTC | Fixed bug that made an assertion fail with the -M option | 29 June 2015, 16:07:37 UTC |
| e7c990d | stamatak | 25 June 2015, 08:21:30 UTC | fixed major bug in likelihood functions for partitioned analyses with linked branch lengths fixed bug for P-Invar models | 25 June 2015, 08:21:30 UTC |
| 745075d | stamatak | 16 June 2015, 11:04:37 UTC | added some experimental stuff for stephen | 16 June 2015, 11:04:37 UTC |
| da49bd2 | stamatak | 15 June 2015, 06:31:19 UTC | updated manual | 15 June 2015, 06:31:19 UTC |
| e3b3d01 | stamatak | 15 June 2015, 06:22:25 UTC | added option --set-thread-affinity to enable thread pinning for the hybrid MPI/PThreads version | 15 June 2015, 06:22:25 UTC |
| 297bc55 | stamatak | 21 May 2015, 12:19:33 UTC | -fixed bug in BFGS optimization -improved error handling | 21 May 2015, 12:19:33 UTC |
| 053d5f6 | stamatak | 19 April 2015, 12:06:35 UTC | added windowns executables for version 8.1.20 | 19 April 2015, 12:06:35 UTC |
| b9048ea | stamatak | 18 April 2015, 17:08:52 UTC | minor bug fixes | 18 April 2015, 17:08:52 UTC |
| d98c99c | stamatak | 16 April 2015, 16:01:31 UTC | fixed a stupid mistake | 16 April 2015, 16:01:31 UTC |
| 40670a5 | stamatak | 15 April 2015, 14:40:19 UTC | -added flags for computing JC69 and K80 DNA models -added an experimental option for ascertainment bias correction that takes into account missing data | 15 April 2015, 14:40:19 UTC |
| 74ecbe9 | stamatak | 15 April 2015, 14:39:48 UTC | updated manual | 15 April 2015, 14:39:48 UTC |
| 440a1f5 | stamatak | 13 April 2015, 08:48:58 UTC | Added Windows executables | 13 April 2015, 08:48:58 UTC |
| 903de58 | stamatak | 10 April 2015, 13:35:09 UTC | updated version number in readme and release notes | 10 April 2015, 13:35:09 UTC |
| 411e39b | stamatak | 10 April 2015, 13:33:00 UTC | -added ancestral state computation for LG4X and LG4M models -improved partition parser error reporting -added check for preventing users to specify one of the -f options multiple times -imrpoved error checking in file copy of MPI version | 10 April 2015, 13:33:00 UTC |
| cb84ec2 | stamatak | 08 February 2015, 10:42:52 UTC | added expliciit offendimng site printout for invariable sites that are in partitions that are to be analyzed using an ascertainment bias correction | 08 February 2015, 10:42:52 UTC |
| 53e5f18 | stamatak | 19 January 2015, 12:24:18 UTC | When not specifying the number of threads via -T in the PThreads option, RAxML will now set the number of threads to 2 by default. | 19 January 2015, 12:24:18 UTC |
| 0c4847f | stamatak | 05 January 2015, 17:34:06 UTC | added version 8.1.15 Windows executables kindly provided by William Gearty | 05 January 2015, 17:34:06 UTC |
| 24e8e40 | stamatak | 27 December 2014, 20:09:06 UTC | small, unimportant bug fix | 27 December 2014, 20:09:06 UTC |
| 31501e7 | stamatak | 27 December 2014, 19:10:02 UTC | added new protein subst model stmtREV, see: http://datadryad.org/resource/doi:10.5061/dryad.7b470 | 27 December 2014, 19:10:02 UTC |
| a25e3a0 | stamatak | 22 December 2014, 14:58:48 UTC | --flag-check option now also writes output into a file called RAxML_flagCheck | 22 December 2014, 14:58:48 UTC |
| 52d3f18 | stamatak | 19 December 2014, 13:38:15 UTC | -added some additional error checking for partitions and the EPA algorithm, to prevent users from doing things wrong | 19 December 2014, 13:38:15 UTC |
| 81a791f | stamatak | 18 December 2014, 18:33:23 UTC | added v 8.1.13 windows executables | 18 December 2014, 18:33:23 UTC |
| 04ae5d2 | stamatak | 17 December 2014, 08:06:15 UTC | added dll file to new windows executables | 17 December 2014, 08:06:15 UTC |
| f72f782 | stamatak | 17 December 2014, 08:04:04 UTC | Added Windows executables for version 8.1.11 | 17 December 2014, 08:04:04 UTC |
| 9706247 | stamatak | 16 December 2014, 14:08:33 UTC | fixed a bug in lewis correction for asc. bias | 16 December 2014, 14:08:33 UTC |
| cd236b5 | stamatak | 12 December 2014, 15:56:29 UTC | fixed the bugs introduced by the bug fix | 12 December 2014, 15:56:29 UTC |
| 97a901d | stamatak | 12 December 2014, 15:50:29 UTC | fixed a bug in lewis ascertainment bias correction, the likelihoods were not correctly scaled in evaluateGeneric() | 12 December 2014, 15:50:29 UTC |
| 041e083 | stamatak | 11 December 2014, 15:45:13 UTC | fixed small bug in LG4X model when writeVector is set to TRUE | 11 December 2014, 15:45:13 UTC |
| 0816615 | stamatak | 10 December 2014, 21:42:42 UTC | fixed some issues with undetermined sites supression | 10 December 2014, 21:42:42 UTC |
| 13a6f4c | stamatak | 10 December 2014, 17:29:20 UTC | added functionality to automatically remove fully undetermined sites from the alignment | 10 December 2014, 17:29:20 UTC |
| 7430f22 | Alexis Stamatakis | 08 December 2014, 12:42:48 UTC | Merge pull request #17 from wookietreiber/master use more portabel perl shebangs | 08 December 2014, 12:42:48 UTC |
| 1ea2418 | Christian Krause | 07 December 2014, 12:09:06 UTC | use more portabel perl shebangs use `/usr/bin/env perl` instead of `/usr/local/bin/perl` as it finds perl in non-hard-coded locations | 07 December 2014, 12:09:06 UTC |
| fe7c8a9 | stamatak | 05 December 2014, 18:05:02 UTC | fixed a bug in the parser | 05 December 2014, 18:05:02 UTC |
| 203f9b8 | stamatak | 05 December 2014, 17:37:49 UTC | fixed some errors in the protein model selection test | 05 December 2014, 17:37:49 UTC |
| 427762d | stamatak | 05 December 2014, 16:00:43 UTC | update version numbers | 05 December 2014, 16:00:43 UTC |
| e7f0ed4 | stamatak | 05 December 2014, 15:43:56 UTC | fixed a problem in the auto prot output | 05 December 2014, 15:43:56 UTC |
| 36ec4a9 | stamatak | 05 December 2014, 14:19:56 UTC | small fixes for auto protein | 05 December 2014, 14:19:56 UTC |
| 3e0e1f5 | stamatak | 05 December 2014, 11:00:49 UTC | updated manual | 05 December 2014, 11:00:49 UTC |
| f6656d6 | stamatak | 02 December 2014, 10:52:46 UTC | updated manual | 02 December 2014, 10:52:46 UTC |
| f3ea3d6 | stamatak | 28 November 2014, 14:06:22 UTC | -added two additional ways for correcting ascertainment bias. Both new methods can be used to correct for the absence of invariable sites, when the number of invariable sites of the dataset is known. | 28 November 2014, 14:06:22 UTC |
| 03479cc | stamatak | 28 November 2014, 14:05:30 UTC | updated manual | 28 November 2014, 14:05:30 UTC |
| 5a695ce | stamatak | 26 November 2014, 07:29:06 UTC | fixed a bug in the Pthreads version of the evolutionary placement algorithm (EPA) that occured under the CAT model. | 26 November 2014, 07:29:06 UTC |
