Sequence filename : /auto/dufayard/res/parc_wim/proteic_M2624_139x348_2006.phy Data type : aa Sequence format : interleaved Number of data sets : 1 Nb of bootstrapped data sets : 0 Model name : WAG Proportion of invariable sites : 0.000000 Number of subst. rate categs : 4 Gamma distribution parameter : estimated Starting tree : BIONJ Optimise tree topology : yes Optimise branch lengths and rate parameters : yes . Compressing sequences... . Computing pairwise distances... . Large distance encountered between tax84 and tax19 sequences . Building BIONJ tree... N_RGRFT: 55 N_GLOBL: 27 MAX_DIST: 27 . Large distance encountered between tax84 and tax19 sequences . Log(lk) : * -> -13921.129611 . Log(lk) : -13921.129611 -> -13604.232506 18 swaps done . Log(lk) : -13604.232506 -> -13498.258043 15 swaps done . Log(lk) : -13498.258043 -> -13427.310756 13 swaps done . Optimisation of the gamma shape parameter... . Log(lk) : -13318.688896 -> -13268.792204 10 swaps done . Log(lk) : -13268.792204 -> -13242.850803 6 swaps done . Log(lk) : -13242.850803 -> -13223.183816 6 swaps done . Log(lk) : -13223.183816 -> -13214.499492 6 swaps done . Optimisation of the gamma shape parameter... . Log(lk) : -13214.451525 -> -13200.581150 6 swaps done . Log(lk) : -13200.581150 -> -13197.787150 4 swaps done . Log(lk) : -13197.787150 -> -13189.665574 4 swaps done . Log(lk) : -13189.665574 -> -13187.850843 3 swaps done . Optimisation of the gamma shape parameter... . Log(lk) : -13187.847889 -> -13185.020245 3 swaps done . Log(lk) : -13185.020245 -> -13185.612624 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the gamma shape parameter... . Log(lk) : -13185.020245 -> -13182.600670 3 swaps done . Log(lk) : -13182.600670 -> -13181.620903 3 swaps done . Optimisation of the gamma shape parameter... . Log(lk) : -13181.620829 -> -13170.668986 1 swap done . Log(lk) : -13170.668986 -> -13166.741738 1 swap done . Log(lk) : -13166.741738 -> -13166.131023 1 swap done . Log(lk) : -13166.131023 -> -13165.934432 2 swaps done . Optimisation of the gamma shape parameter... . Log(lk) : -13165.934202 -> -13165.838791 1 swap done . Log(lk) : -13165.838791 -> -13165.767370 0 swap done . Log(lk) : -13165.767370 -> -13165.704775 0 swap done . Log(lk) : -13165.704775 -> -13165.647328 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -13165.647328 -> -13165.537672 1 swap done . Log(lk) : -13165.537672 -> -13165.410857 0 swap done . Log(lk) : -13165.410857 -> -13165.368068 0 swap done . Log(lk) : -13165.368068 -> -13165.331263 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -13165.331261 -> -13165.297661 0 swap done . Log(lk) : -13165.297661 -> -13165.265273 0 swap done . Log(lk) : -13165.265273 -> -13165.234370 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 17 -> 28 (0.243515) making move: 23 -> 13 (0.735756) making move: 31 -> 23 (0.110973) making move: 32 -> 88 (0.394660) making move: 36 -> 23 (0.580066) making move: 37 -> 270 (28.405865) making move: 38 -> 139 (7.500780) making move: 39 -> 6 (0.536795) making move: 76 -> 74 (0.011863) making move: 90 -> 247 (2.424251) making move: 141 -> 32 (4.313004) making move: 167 -> 222 (0.957834) making move: 186 -> 77 (14.200845) making move: 187 -> 179 (2.191147) making move: 188 -> 189 (0.170408) making move: 192 -> 71 (14.342375) making move: 227 -> 50 (4.901957) making move: 235 -> 70 (16.162067) making move: 238 -> 140 (29.900192) making move: 244 -> 31 (5.722351) making move: 245 -> 208 (30.510007) making move: 246 -> 36 (0.218209) making move: 251 -> 12 (5.045443) making move: 255 -> 260 (0.633812) making move: 268 -> 249 (1.679004) making move: 269 -> 37 (4.364724) making move: 270 -> 260 (9.748637) making move: 271 -> 266 (0.229523) Log (lk): -12927.535617 . Log(lk) : -12927.535617 -> -12917.571142 9 swaps done . Optimisation of the gamma shape parameter... . Log(lk) : -12917.569208 -> -12907.108555 6 swaps done . Log(lk) : -12907.108555 -> -12900.998684 4 swaps done . Log(lk) : -12900.998684 -> -12900.480834 4 swaps done . Log(lk) : -12900.480834 -> -12899.426296 3 swaps done . Optimisation of the gamma shape parameter... . Log(lk) : -12899.425643 -> -12900.924138 3 swaps done . Moving backward (topology + branch lengths) . Optimisation of the gamma shape parameter... . Log(lk) : -12899.425643 -> -12895.654033 3 swaps done . Log(lk) : -12895.654033 -> -12895.010220 1 swap done . Log(lk) : -12895.010220 -> -12894.878755 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -12894.878729 -> -12894.837267 0 swap done . Log(lk) : -12894.837267 -> -12894.820603 0 swap done . Log(lk) : -12894.820603 -> -12894.811314 0 swap done . Log(lk) : -12894.811314 -> -12894.804893 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -12894.804891 -> -12894.799559 1 swap done . Log(lk) : -12894.799559 -> -12894.794190 0 swap done . Log(lk) : -12894.794190 -> -12894.790332 0 swap done . Log(lk) : -12894.790332 -> -12894.787024 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -12894.787023 -> -12894.784088 0 swap done . Log(lk) : -12894.784088 -> -12894.781439 0 swap done . Log(lk) : -12894.781439 -> -12894.779016 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 10 -> 31 (0.080646) making move: 32 -> 243 (0.051234) making move: 141 -> 227 (2.274403) making move: 245 -> 184 (7.397384) making move: 246 -> 31 (0.570578) Log (lk): -12878.076363 . Log(lk) : -12878.076363 -> -12876.598224 1 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -12876.593961 -> -12874.371246 2 swaps done . Log(lk) : -12874.371246 -> -12873.860940 1 swap done . Log(lk) : -12873.860940 -> -12873.654184 0 swap done . Log(lk) : -12873.654184 -> -12873.513954 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -12873.513948 -> -12873.413307 0 swap done . Log(lk) : -12873.413307 -> -12873.338784 0 swap done . Log(lk) : -12873.338784 -> -12873.282670 0 swap done . Log(lk) : -12873.282670 -> -12873.239547 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 245 -> 162 (0.425732) Log (lk): -12872.054688 . Optimisation of the gamma shape parameter... . Log(lk) : -12872.054052 -> -12871.944965 1 swap done . Log(lk) : -12871.944965 -> -12871.925893 0 swap done . Log(lk) : -12871.925893 -> -12871.918032 0 swap done . Log(lk) : -12871.918032 -> -12871.914040 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -12871.914039 -> -12871.911819 0 swap done . Log(lk) : -12871.911819 -> -12871.910828 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods making move: 178 -> 180 (0.054763) Log (lk): -12871.272157 . Log(lk) : -12871.272157 -> -12871.254026 1 swap done . Log(lk) : -12871.254026 -> -12870.929176 2 swaps done . Optimisation of the gamma shape parameter... . Log(lk) : -12870.929175 -> -12870.619295 1 swap done . Log(lk) : -12870.619295 -> -12870.478439 1 swap done . Log(lk) : -12870.478439 -> -12870.447801 2 swaps done . Log(lk) : -12870.447801 -> -12870.427981 1 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -12870.427979 -> -12870.440661 1 swap done . Moving backward (topology + branch lengths) . Optimisation of the gamma shape parameter... . Log(lk) : -12870.427979 -> -12870.411778 1 swap done . Log(lk) : -12870.411778 -> -12870.402355 0 swap done . Log(lk) : -12870.402355 -> -12870.401206 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -12870.401206 -> -12870.400794 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations making move: 167 -> 228 (0.925693) Log (lk): -12869.382144 . Log(lk) : -12869.382144 -> -12868.952200 1 swap done . Log(lk) : -12868.952200 -> -12868.786862 0 swap done . Log(lk) : -12868.786862 -> -12868.701057 0 swap done . Optimisation of the gamma shape parameter... . Log(lk) : -12868.701052 -> -12868.655648 0 swap done . Log(lk) : -12868.655648 -> -12868.630851 0 swap done . Log(lk) : -12868.630851 -> -12868.615274 0 swap done . Log(lk) : -12868.615274 -> -12868.604970 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 115 -> 111 (0.009912) Log (lk): -12868.588459 . Optimisation of the gamma shape parameter... . Log(lk) : -12868.588459 -> -12868.586844 1 swap done . Log(lk) : -12868.586844 -> -12868.586074 0 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization making move: 115 -> 112 (0.000592) Log (lk): -12868.585200 . Log(lk) : -12868.585200 -> -12868.584849 1 swap done Trying SPR moves -calculating tree distances and estimating likelihoods -performing local edge length optimizations -performing global edge length optimization Log (lk): -12868.585516 nr_d_L: 589108 nr_d_lk: 133081 nr_loc: 313 nr_glb: 29 . Time used 1h54m40s %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 6479.64user 0.00system 1:54:40elapsed 94%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps