| f4ce699 | stamatak | 06 June 2014, 14:07:35 UTC | added a more elaborate function for imputing missing sequence data. Needs to be activated by uncommenting: #define _SUBTREE_PREDICTION in axml.c | 06 June 2014, 14:07:35 UTC |
| 934296f | stamatak | 23 May 2014, 09:26:50 UTC | updated manual | 23 May 2014, 09:26:50 UTC |
| 03e580a | stamatak | 06 May 2014, 16:30:03 UTC | fixed an assertion that shall not fail when bootstrapping using a wieght file | 06 May 2014, 16:30:03 UTC |
| 82fa3b5 | stamatak | 06 May 2014, 15:38:12 UTC | added windows executables for v 8.0.20 kindly provided by Ingo Michalak :-) | 06 May 2014, 15:38:12 UTC |
| b7b849d | stamatak | 06 May 2014, 15:29:37 UTC | fixed a bug in the tree string processing | 06 May 2014, 15:29:37 UTC |
| 6c39ac9 | stamatak | 18 April 2014, 06:31:58 UTC | updated manual | 18 April 2014, 06:31:58 UTC |
| a6506ee | stamatak | 13 April 2014, 08:48:49 UTC | fixed minor type casting issues and minor bug in error detection output message | 13 April 2014, 08:48:49 UTC |
| c343283 | stamatak | 28 March 2014, 09:43:16 UTC | 1. fixed a bug in the LG4X protein substitution model 2. fixed a bug for the ascertainment bias correction calculation with partitioned datasets | 28 March 2014, 09:43:16 UTC |
| 7df9705 | stamatak | 27 March 2014, 14:06:11 UTC | uncommented the wrong debug flag commented the correct debug flag | 27 March 2014, 14:06:11 UTC |
| dcbe679 | stamatak | 27 March 2014, 14:03:02 UTC | commented a debug flag | 27 March 2014, 14:03:02 UTC |
| 4a1e9e2 | stamatak | 27 March 2014, 14:00:59 UTC | -fixed a bug in the error checking function -cleaned up the code a bit | 27 March 2014, 14:00:59 UTC |
| 1bf43c6 | stamatak | 26 March 2014, 10:26:27 UTC | -fixed a typo in a warning | 26 March 2014, 10:26:27 UTC |
| 334c163 | stamatak | 25 March 2014, 17:31:05 UTC | updated windows executables | 25 March 2014, 17:31:05 UTC |
| a693459 | stamatak | 25 March 2014, 16:19:31 UTC | Fixed bugs in: 1. The PThreads version of the evolutionary placement algorithm 2. The calculation of SH-like support values | 25 March 2014, 16:19:31 UTC |
| 38cb4d1 | stamatak | 25 March 2014, 11:29:01 UTC | Fixed Makefiles for Macintosh using clang compiler. | 25 March 2014, 11:29:01 UTC |
| 623387c | stamatak | 22 March 2014, 07:23:39 UTC | added readme to windows executables directory | 22 March 2014, 07:23:39 UTC |
| b526883 | stamatak | 22 March 2014, 07:22:17 UTC | updated windows executables | 22 March 2014, 07:22:17 UTC |
| c18cc11 | stamatak | 21 March 2014, 13:04:07 UTC | updated manual | 21 March 2014, 13:04:07 UTC |
| 5361156 | stamatak | 19 March 2014, 17:09:54 UTC | fixed some typos in the printouts, made the makefiles debian compliant | 19 March 2014, 17:09:54 UTC |
| ef51969 | stamatak | 16 March 2014, 17:36:50 UTC | added directory with some windows executables compiled by Ingo Michalak. | 16 March 2014, 17:36:50 UTC |
| e12b993 | stamatak | 13 March 2014, 17:16:30 UTC | removed some unnecessary source files. | 13 March 2014, 17:16:30 UTC |
| 2221aa2 | stamatak | 12 March 2014, 17:22:16 UTC | added some source code documentation | 12 March 2014, 17:22:16 UTC |
| 2fb2ec2 | stamatak | 11 March 2014, 19:34:50 UTC | fixed a bug in the fast tree search algorithm (-f E) option. | 11 March 2014, 19:34:50 UTC |
| 6745b06 | stamatak | 11 March 2014, 18:58:19 UTC | updated manual | 11 March 2014, 18:58:19 UTC |
| a869b6b | stamatak | 11 March 2014, 16:40:26 UTC | updated version numbers | 11 March 2014, 16:40:26 UTC |
| 4f1b8ce | stamatak | 11 March 2014, 16:38:40 UTC | bug fixes in fasta file pasring and LG4X model. | 11 March 2014, 16:38:40 UTC |
| 010c3b4 | stamatak | 11 March 2014, 16:22:10 UTC | updated manual | 11 March 2014, 16:22:10 UTC |
| 693b12f | stamatak | 06 March 2014, 17:43:40 UTC | improved error reporting in partition file parser. | 06 March 2014, 17:43:40 UTC |
| 9f2378a | stamatak | 05 March 2014, 15:54:28 UTC | added some additional checks for the base frequency range to prevent potential numerical problems. | 05 March 2014, 15:54:28 UTC |
| 5b1f6aa | stamatak | 04 March 2014, 16:56:04 UTC | improved the error checking for the LnL tolerance in model parameter optimization routine. The tolerance is not hard-coded but a function of the LnL score now. | 04 March 2014, 16:56:04 UTC |
| 6e8356e | stamatak | 28 February 2014, 14:41:15 UTC | minor fix such that the -f B option works again, this was broken by the introduction of the ML estimate of base frequencies. | 28 February 2014, 14:41:15 UTC |
| da95c3f | stamatak | 28 February 2014, 14:08:20 UTC | updated manual | 28 February 2014, 14:08:20 UTC |
| 5cc79f6 | stamatak | 28 February 2014, 12:33:05 UTC | Fixed an issue with an assertion for the likelihood calculations that failed. The assertion was placed incorrectly. | 28 February 2014, 12:33:05 UTC |
| 145f77e | stamatak | 28 February 2014, 08:01:19 UTC | updated manual | 28 February 2014, 08:01:19 UTC |
| d127945 | stamatak | 27 February 2014, 12:26:38 UTC | made the error diagnosis for tree file parsing more verbose and understandable, RAxML will now also exit with an error when instead of a tree file you have specified an alignment file | 27 February 2014, 12:26:38 UTC |
| eb5a100 | stamatak | 25 February 2014, 19:23:09 UTC | updated manual | 25 February 2014, 19:23:09 UTC |
| a281249 | stamatak | 25 February 2014, 19:05:19 UTC | added a compiler flag to allow calculating TC/IC scores as described in the following paper: L. Salichos, A. Stamatakis, A. Rokas: "Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees". In Molecular Biology and Evolution, 2014. By default RAxML computes TC/IC scores a bit differently, please read the RAxML manual for further details. | 25 February 2014, 19:05:19 UTC |
| 933bc73 | stamatak | 19 February 2014, 16:05:19 UTC | added better error reporting for cases where RAxML runs out of memory | 19 February 2014, 16:05:19 UTC |
| dd40860 | stamatak | 05 February 2014, 12:31:19 UTC | added option to output the number of unique trees in the pairwise RF distance calculation (-f r) option | 05 February 2014, 12:31:19 UTC |
| 041014c | stamatak | 04 February 2014, 14:58:37 UTC | updated manual | 04 February 2014, 14:58:37 UTC |
| 4257e5a | stamatak | 04 February 2014, 13:53:42 UTC | added some routines to implement multiparameter bfgs optimization, the routines are not called yet | 04 February 2014, 13:53:42 UTC |
| 7c0ecc7 | stamatak | 30 January 2014, 09:40:38 UTC | fixed bug in script: applyRAxML2AllFilesInDirectory.pl | 30 January 2014, 09:40:38 UTC |
| d6f96b8 | stamatak | 29 January 2014, 17:07:46 UTC | updated manual | 29 January 2014, 17:07:46 UTC |
| e6f2196 | stamatak | 27 January 2014, 13:20:40 UTC | optimized memory utilization of Pthreads version | 27 January 2014, 13:20:40 UTC |
| dbb464b | stamatak | 25 January 2014, 17:53:49 UTC | updated manual | 25 January 2014, 17:53:49 UTC |
| e7e44a2 | stamatak | 23 January 2014, 14:14:31 UTC | updated manual | 23 January 2014, 14:14:31 UTC |
| 195ec49 | stamatak | 23 January 2014, 14:05:51 UTC | version number update | 23 January 2014, 14:05:51 UTC |
| 410a877 | stamatak | 23 January 2014, 14:05:07 UTC | -added new option -f k | 23 January 2014, 14:05:07 UTC |
| 5a4b061 | stamatak | 23 January 2014, 10:33:02 UTC | updated clang-based makefiles for MACs | 23 January 2014, 10:33:02 UTC |
| 1765d76 | stamatak | 23 January 2014, 10:19:26 UTC | -updated manual | 23 January 2014, 10:19:26 UTC |
| e2f54b2 | stamatak | 16 January 2014, 11:23:57 UTC | changed source file permissions | 16 January 2014, 11:23:57 UTC |
| bee511b | stamatak | 14 January 2014, 15:21:51 UTC | -added a warning that will inform users when high alpha values are being estimated by RAxML, meaning that they maybe should (i) conduct a model test (ii) use a plain model of substitution. This often seems to happen with SNP datasets | 14 January 2014, 15:21:51 UTC |
| 19d6cd9 | stamatak | 14 January 2014, 12:12:52 UTC | fixed a bug in the ascertainment bias correction under the CAT model of rate heterogeneity and updated the manual a bit | 14 January 2014, 12:12:52 UTC |
| 5e7c429 | stamatak | 19 December 2013, 15:34:11 UTC | fixed a type on the manual | 19 December 2013, 15:34:11 UTC |
| c1225ae | stamatak | 19 December 2013, 11:17:15 UTC | first full version of the new manual | 19 December 2013, 11:17:15 UTC |
| ca1c277 | stamatak | 18 December 2013, 15:26:08 UTC | finished editing manual for today | 18 December 2013, 15:26:08 UTC |
| ede0b8a | stamatak | 18 December 2013, 09:53:06 UTC | continued editing the new manual | 18 December 2013, 09:53:06 UTC |
| a73f315 | stamatak | 16 December 2013, 16:10:59 UTC | edited the manual a bit, enough for today | 16 December 2013, 16:10:59 UTC |
| dd94432 | stamatak | 16 December 2013, 12:17:06 UTC | -started drafting new manual | 16 December 2013, 12:17:06 UTC |
| 6d56ab5 | stamatak | 13 December 2013, 13:48:40 UTC | -put eigenvalue/eigenvector decomposition into separate file that is compiled without any compiler optimizations such as to avoid recurrent (potential) trouble with the Intel icc compiler that over-optimized these functions and yielded them numerically instable -add fix by the UF HPC center for better pthreads scheduling in the hybrid MPI/Pthreads version | 13 December 2013, 13:48:40 UTC |
| 0227ddf | stamatak | 12 December 2013, 14:31:38 UTC | fixed a little bug | 12 December 2013, 14:31:38 UTC |
| 39113d0 | stamatak | 12 December 2013, 14:29:27 UTC | fixed a bug in the Pthreads implementation of ascertainment bias correction | 12 December 2013, 14:29:27 UTC |
| bc073f3 | stamatak | 12 December 2013, 13:18:03 UTC | added a function to free memory for likelihood calculations that is not required any more for the Pthreads version of the EPA algorithm at the placement stage. | 12 December 2013, 13:18:03 UTC |
| 2c0a8ef | stamatak | 10 December 2013, 13:39:17 UTC | 1. added ascertainment bias correction for CAT model of rate heterogeneity. 2. The cat model can also be transformed into a plain model that does not use rate heterogeneity at all by specifying -m GTRCAT and -V, this combination corresponds to a plain GTR model | 10 December 2013, 13:39:17 UTC |
| 4cc2853 | stamatak | 10 December 2013, 08:38:01 UTC | output cosmetics | 10 December 2013, 08:38:01 UTC |
| dc6747b | stamatak | 10 December 2013, 08:26:11 UTC | updated help and usage messages | 10 December 2013, 08:26:11 UTC |
| 1121cc8 | stamatak | 09 December 2013, 19:57:59 UTC | -added -H option that allows to disable pattern compression -I now allow the EPA to also be re-started from a binary model checkpoint when the CAT model is being used | 09 December 2013, 19:57:59 UTC |
| 4f82322 | stamatak | 06 December 2013, 12:05:29 UTC | -added directory with some small and hopefully helpful perl scripts | 06 December 2013, 12:05:29 UTC |
| 7922d3a | stamatak | 25 November 2013, 09:37:33 UTC | updated version number | 25 November 2013, 09:37:33 UTC |
| f698166 | stamatak | 25 November 2013, 09:35:58 UTC | substantially optimized the tree parsing function for the tree plausibility checker (-f R) option. Execution times decrease from 124 to 2.4 seconds :-) | 25 November 2013, 09:35:58 UTC |
| 58b4543 | stamatak | 24 November 2013, 10:28:04 UTC | small optimziation of plausibility checker performance | 24 November 2013, 10:28:04 UTC |
| 64a2045 | stamatak | 24 November 2013, 10:13:02 UTC | fixed a bug in the plausibility checker code | 24 November 2013, 10:13:02 UTC |
| 84f5ffd | stamatak | 22 November 2013, 16:53:28 UTC | improved version of david's plausibility checker algorithm | 22 November 2013, 16:53:28 UTC |
| cbe6887 | stamatak | 22 November 2013, 09:19:00 UTC | integrated david dao's faster implementation of the plausibility checker algorithm (-f R option) | 22 November 2013, 09:19:00 UTC |
| 198ca23 | stamatak | 18 November 2013, 13:20:07 UTC | -minor bug fix | 18 November 2013, 13:20:07 UTC |
| 5aa54b0 | stamatak | 18 November 2013, 12:33:21 UTC | minor bug fix that caused an assertion to fail | 18 November 2013, 12:33:21 UTC |
| 980f94b | stamatak | 16 November 2013, 15:33:12 UTC | removed -g flag from AVX makefile | 16 November 2013, 15:33:12 UTC |
| 20fd4f5 | stamatak | 16 November 2013, 15:30:20 UTC | -added a NUMA architecture optimization for the PThreads version of the EPA algorithm -fixed a bug in the AVX-based likelihood functions of the EPA algorithm in the CAT model | 16 November 2013, 15:30:20 UTC |
| 855c847 | stamatak | 16 November 2013, 14:37:55 UTC | MPI and hybrid MPI/Pthreads versions now also support RELL bootstraps. | 16 November 2013, 14:37:55 UTC |
| a72ff63 | stamatak | 15 November 2013, 10:08:33 UTC | small fix to a constant, should do 1000 RELL resamples instead of 100 by default. | 15 November 2013, 10:08:33 UTC |
| cdc551a | stamatak | 15 November 2013, 10:05:32 UTC | Added ultra-fast RELL bootstrapping that can be invoked via -f D as described in the following paper: B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultra-Fast Approximation for Phylogenetic Bootstrap. Mol. Biol. Evol., 30, 1188-1195. It does not work yet with the MPI, nor the hybrid MPI/PThreads version and is still in the test phase! | 15 November 2013, 10:05:32 UTC |
| 7c81076 | stamatak | 13 November 2013, 10:27:35 UTC | general cleanup of random number generators | 13 November 2013, 10:27:35 UTC |
| ffc3f70 | stamatak | 11 November 2013, 11:37:02 UTC | additional fix for plausibility checker | 11 November 2013, 11:37:02 UTC |
| c96c9ba | stamatak | 11 November 2013, 11:06:48 UTC | -fixed small bug in tree plausibility check function | 11 November 2013, 11:06:48 UTC |
| be41fd7 | stamatak | 07 November 2013, 19:10:39 UTC | Added support for multi-state models in Pthreads version of Evolutionary Placement Algorithm (EPA) | 07 November 2013, 19:10:39 UTC |
| f30b37d | stamatak | 01 November 2013, 14:18:18 UTC | small cosmetic correction | 01 November 2013, 14:18:18 UTC |
| 3f50ca6 | stamatak | 01 November 2013, 14:13:44 UTC | 1. added an error check for partitions with ascertainment bias correction. RAxML will now check if there are non-variable sites in the partition for which the user requests a correction. 2. slightly corrected likelihood calculations in branch length optimization routine | 01 November 2013, 14:13:44 UTC |
| 3d9d595 | stamatak | 29 October 2013, 09:21:39 UTC | Integrated a patch by Akifumi Tanabe in mem_alloc.c to compile RAxML on Windows. To compile, the code requires the MinGW-w64 GCC compiler and the "-lpthread" option to be appended to LIBRARIES in the respective Makefiles. | 29 October 2013, 09:21:39 UTC |
| 0c130fe | stamatak | 29 October 2013, 09:12:22 UTC | Added substitution models that use the ascertainment bias, also know as Lewis correction. They are invoked like the standard models, with an ASC_ prefix, for instance, -m ASC_GTRGAMMA or -m ASC_BINGAMMA. Note that, in some cases numerical problems might occur, it's currently unclear whether this is an implementation issue or a theoretical issue with the correction. However, it seems to rather be a theoretical problem. | 29 October 2013, 09:12:22 UTC |
| 635db36 | stamatak | 18 October 2013, 09:20:17 UTC | -integrated Alexey's fix for more efficient putput file generation for the Evolutionary Placement Algorithm | 18 October 2013, 09:20:17 UTC |
| ab67455 | stamatak | 17 October 2013, 15:35:28 UTC | 1. fixed and activated code for using fused multiply-add AVX2 instructions 2. this only works on Intel Haswell and AMD Bulldozer architectures 3. it requires gcc v4.7 or greater 4. added respective makefiles 5. still needs testing on MACS 6. the speed improvements are not great, but one may see 5-10%. | 17 October 2013, 15:35:28 UTC |
| 1ea3e7a | stamatak | 09 October 2013, 10:38:14 UTC | small modif | 09 October 2013, 10:38:14 UTC |
| 748fdf2 | stamatak | 09 October 2013, 10:33:58 UTC | integrated options to conduct ML estimate/optimization of base frequencies | 09 October 2013, 10:33:58 UTC |
| 27d7956 | stamatak | 20 September 2013, 08:40:02 UTC | -small cosmetic changes, not worth a version number update | 20 September 2013, 08:40:02 UTC |
| b6050f9 | stamatak | 06 September 2013, 14:03:25 UTC | -major code cleanup in model optimization routines | 06 September 2013, 14:03:25 UTC |
| a60a3ff | stamatak | 30 August 2013, 09:16:47 UTC | Integrated Andre's fix for proper memory cleanup/deallocation in the consensus tree routines. | 30 August 2013, 09:16:47 UTC |
| f15ca0a | stamatak | 29 August 2013, 13:56:26 UTC | fixed bug in tree parsing routines for multi-furcating trees | 29 August 2013, 13:56:26 UTC |
| 7a7e5e3 | stamatak | 21 August 2013, 14:15:53 UTC | added additional error checks to prevent users from applying functions for discrete operations on trees to tree sets that just contain a single tree. | 21 August 2013, 14:15:53 UTC |
| f7ad21a | stamatak | 20 August 2013, 10:20:06 UTC | removed some debuc output | 20 August 2013, 10:20:06 UTC |
| 7760aed | stamatak | 20 August 2013, 10:19:09 UTC | corrected a typo. | 20 August 2013, 10:19:09 UTC |
