.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1379_9x1557_2003.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 . 'Middle' of each rate class : mean . Amino acid equilibrium frequencies : model . Optimise tree topology : yes . Tree topology search : Best of NNIs and SPRs . Starting tree : BioNJ . Add random input tree : yes . Number of random starting trees : 5 . Optimise branch lengths : yes . Optimise substitution model parameters : yes . Run ID : none oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo . Compressing sequences... . 720 patterns found. (out of a total of 1557 sites) . 838 sites without polymorphism (53.82%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 13Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13340.7520] [Alpha ][ 0.500960] . ( 0 sec) [ -13329.4253] [ 1433] [depth= 2] . ( 1 sec) [ -13034.6309] [ 1483] [depth= 2] . ( 1 sec) [ -12858.6830] [ 1473] [depth= 2] . ( 1 sec) [ -12702.4552] [ 1467] [depth= 1] . ( 2 sec) [ -12439.6635] [ 1473] [depth= 1] . ( 2 sec) [ -12433.9860] [ 1467] [depth= 2] . ( 3 sec) [ -12414.7847] [ 1471] [depth= 1] . ( 3 sec) [ -11726.2151] [ 1361] [depth= 1] . ( 4 sec) [ -11718.9511] [ 1365] [depth= 1] . ( 5 sec) [ -11712.2128] [ 1363] [depth= 1] . ( 5 sec) [ -11705.7128] [ 1356] [depth= 1] . ( 6 sec) [ -11647.8298] [Branch lengths ] . ( 7 sec) [ -11645.6424] [Alpha ][ 0.589719] . ( 9 sec) [ -11644.7065] [ 1352] [depth= 1] . ( 10 sec) [ -11628.1239] [ 1354] [depth= 3] . ( 10 sec) [ -11624.5961] [ 1349] [depth= 1] . ( 16 sec) [ -11620.2840] [Branch lengths ] . ( 16 sec) [ -11620.2687] [Alpha ][ 0.598104] . ( 26 sec) [ -11620.1630] [Branch lengths ] . ( 26 sec) [ -11620.1630] [Topology ] . ( 27 sec) [ -11620.1509] [Topology ] . ( 28 sec) [ -11620.1486] [Topology ] . ( 29 sec) [ -11620.1480] [Topology ] . ( 30 sec) [ -11620.1480] [Alpha ][ 0.598104] . ( 30 sec) [ -11620.1480] [Topology ] . ( 31 sec) [ -11620.1478] [Topology ] . ( 31 sec) [ -11620.1478] [Alpha ][ 0.598104] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11620.147825. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13191.1141] [Alpha ][ 0.500960] . ( 1 sec) [ -12892.2236] [ 1389] [depth= 1] . ( 1 sec) [ -12752.4960] [ 1378] [depth= 2] . ( 1 sec) [ -12727.6589] [ 1377] [depth= 1] . ( 2 sec) [ -12596.2242] [ 1380] [depth= 3] . ( 2 sec) [ -12426.1762] [ 1384] [depth= 1] . ( 2 sec) [ -11980.8260] [ 1359] [depth= 2] . ( 3 sec) [ -11972.3227] [ 1364] [depth= 1] . ( 3 sec) [ -11935.9542] [ 1348] [depth= 4] . ( 4 sec) [ -11924.9362] [ 1349] [depth= 1] . ( 5 sec) [ -11923.9892] [ 1351] [depth= 4] . ( 6 sec) [ -11923.5672] [ 1351] [depth= 1] . ( 6 sec) [ -11653.7408] [Branch lengths ] . ( 7 sec) [ -11651.1158] [Alpha ][ 0.599605] . ( 7 sec) [ -11649.8038] [ 1352] [depth= 1] . ( 7 sec) [ -11646.2278] [ 1352] [depth= 1] . ( 10 sec) [ -11645.3229] [ 1352] [depth= 2] . ( 13 sec) [ -11641.9723] [ 1356] [depth= 1] . ( 13 sec) [ -11626.1527] [ 1354] [depth= 2] . ( 14 sec) [ -11622.9649] [Branch lengths ] . ( 14 sec) [ -11622.9594] [Alpha ][ 0.594963] . ( 16 sec) [ -11622.6776] [ 1349] [depth= 1] . ( 24 sec) [ -11620.1764] [Branch lengths ] . ( 24 sec) [ -11620.1746] [Alpha ][ 0.597835] . ( 34 sec) [ -11620.1488] [Branch lengths ] . ( 34 sec) [ -11620.1488] [Topology ] . ( 35 sec) [ -11620.1480] [Topology ] . ( 35 sec) [ -11620.1480] [Alpha ][ 0.598432] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11620.147975. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -13068.2614] [Alpha ][ 0.500960] . ( 0 sec) [ -12982.8365] [ 1518] [depth= 3] . ( 1 sec) [ -12204.2995] [ 1498] [depth= 4] . ( 1 sec) [ -12155.3931] [ 1486] [depth= 2] . ( 1 sec) [ -12104.4510] [ 1479] [depth= 3] . ( 2 sec) [ -12070.8183] [ 1457] [depth= 2] . ( 2 sec) [ -12023.3779] [ 1439] [depth= 2] . ( 2 sec) [ -11739.4539] [ 1351] [depth= 1] . ( 3 sec) [ -11689.8242] [ 1349] [depth= 4] . ( 3 sec) [ -11688.4286] [ 1351] [depth= 1] . ( 4 sec) [ -11673.7182] [ 1349] [depth= 1] . ( 4 sec) [ -11671.7599] [ 1355] [depth= 1] . ( 5 sec) [ -11639.5950] [ 1349] [depth= 1] . ( 5 sec) [ -11638.6327] [ 1351] [depth= 1] . ( 6 sec) [ -11624.6284] [Branch lengths ] . ( 6 sec) [ -11622.0310] [Alpha ][ 0.595365] . ( 8 sec) [ -11621.8055] [ 1349] [depth= 1] . ( 14 sec) [ -11620.2780] [Branch lengths ] . ( 14 sec) [ -11620.2750] [Alpha ][ 0.599028] . ( 24 sec) [ -11620.1535] [Branch lengths ] . ( 24 sec) [ -11620.1535] [Topology ] . ( 25 sec) [ -11620.1492] [Topology ] . ( 26 sec) [ -11620.1483] [Topology ] . ( 26 sec) [ -11620.1481] [Alpha ][ 0.598141] . ( 26 sec) [ -11620.1481] [Topology ] . ( 27 sec) [ -11620.1479] [Topology ] . ( 27 sec) [ -11620.1479] [Alpha ][ 0.598141] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11620.147862. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -16181.9257] [Alpha ][ 0.500960] . ( 0 sec) [ -15956.0248] [ 1531] [depth= 1] . ( 1 sec) [ -15764.6627] [ 1495] [depth= 3] . ( 1 sec) [ -15720.2687] [ 1491] [depth= 2] . ( 1 sec) [ -12515.4128] [ 1476] [depth= 3] . ( 2 sec) [ -12366.4098] [ 1477] [depth= 2] . ( 2 sec) [ -12044.6107] [ 1479] [depth= 2] . ( 2 sec) [ -11795.8519] [ 1367] [depth= 1] . ( 2 sec) [ -11784.8923] [ 1355] [depth= 2] . ( 3 sec) [ -11782.8218] [ 1360] [depth= 1] . ( 3 sec) [ -11763.6668] [ 1359] [depth= 1] . ( 5 sec) [ -11731.8642] [ 1356] [depth= 1] . ( 5 sec) [ -11722.7511] [ 1355] [depth= 1] . ( 5 sec) [ -11713.0098] [ 1352] [depth= 3] . ( 6 sec) [ -11643.0777] [Branch lengths ] . ( 6 sec) [ -11640.1885] [Alpha ][ 0.603004] . ( 9 sec) [ -11627.9305] [ 1349] [depth= 3] . ( 10 sec) [ -11625.3943] [ 1351] [depth= 1] . ( 10 sec) [ -11624.5737] [ 1349] [depth= 1] . ( 13 sec) [ -11620.3884] [Branch lengths ] . ( 14 sec) [ -11620.3827] [Alpha ][ 0.598224] . ( 23 sec) [ -11620.1553] [Branch lengths ] . ( 23 sec) [ -11620.1553] [Topology ] . ( 24 sec) [ -11620.1497] [Topology ] . ( 25 sec) [ -11620.1484] [Topology ] . ( 26 sec) [ -11620.1479] [Topology ] . ( 26 sec) [ -11620.1479] [Alpha ][ 0.598224] . ( 27 sec) [ -11620.1479] [Topology ] . ( 28 sec) [ -11620.1478] [Topology ] . ( 28 sec) [ -11620.1478] [Alpha ][ 0.598224] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11620.147809. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -15625.9130] [Alpha ][ 0.500960] . ( 1 sec) [ -15279.4675] [ 1537] [depth= 1] . ( 1 sec) [ -14691.0645] [ 1498] [depth= 3] . ( 1 sec) [ -14402.8382] [ 1374] [depth= 1] . ( 2 sec) [ -13040.8485] [ 1366] [depth= 2] . ( 2 sec) [ -12767.3889] [ 1352] [depth= 1] . ( 2 sec) [ -12575.3931] [ 1355] [depth= 1] . ( 3 sec) [ -12289.0080] [ 1361] [depth= 1] . ( 3 sec) [ -12157.2328] [ 1351] [depth= 4] . ( 3 sec) [ -12088.9442] [ 1348] [depth= 1] . ( 4 sec) [ -12006.8685] [ 1354] [depth= 1] . ( 5 sec) [ -12006.1953] [ 1357] [depth= 2] . ( 5 sec) [ -12003.1737] [ 1362] [depth= 1] . ( 6 sec) [ -12001.4537] [ 1357] [depth= 1] . ( 6 sec) [ -11707.9833] [ 1361] [depth= 2] . ( 7 sec) [ -11647.6598] [Branch lengths ] . ( 7 sec) [ -11645.4932] [Alpha ][ 0.587855] . ( 9 sec) [ -11643.4496] [ 1352] [depth= 1] . ( 10 sec) [ -11642.6442] [ 1356] [depth= 1] . ( 12 sec) [ -11625.0361] [ 1354] [depth= 2] . ( 12 sec) [ -11622.2293] [ 1349] [depth= 1] . ( 17 sec) [ -11620.3818] [Branch lengths ] . ( 17 sec) [ -11620.3491] [Alpha ][ 0.599539] . ( 27 sec) [ -11620.1601] [Branch lengths ] . ( 27 sec) [ -11620.1601] [Topology ] . ( 28 sec) [ -11620.1511] [Topology ] . ( 29 sec) [ -11620.1491] [Topology ] . ( 30 sec) [ -11620.1484] [Topology ] . ( 30 sec) [ -11620.1481] [Alpha ][ 0.598123] . ( 30 sec) [ -11620.1481] [Topology ] . ( 31 sec) [ -11620.1479] [Topology ] . ( 32 sec) [ -11620.1479] [Alpha ][ 0.598123] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -11620.147853. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 0 sec) [ -11696.3996] [Alpha ][ 0.540948] . ( 0 sec) [ -11696.3996] [Topology ] . ( 1 sec) [ -11646.2698] [Topology ] . ( 2 sec) [ -11638.4399] [Topology ] . ( 3 sec) [ -11637.5077] [Topology ] . ( 4 sec) [ -11637.6377] [Topology ] . Moving backward . ( 5 sec) [ -11636.2660] [Topology ] . ( 6 sec) [ -11635.5962] [Topology ] . ( 7 sec) [ -11635.4972] [Topology ] . ( 8 sec) [ -11635.4733] [Topology ] . ( 9 sec) [ -11635.4666] [Topology ] . Checking for NNIs, optimizing five branches... . ( 17 sec) [ -11634.5566] [Alpha ][ 0.600647] . ( 17 sec) [ -11634.5566] [Topology ] . ( 18 sec) [ -11634.5441] [Topology ] . ( 19 sec) [ -11634.5430] [Topology ] . ( 20 sec) [ -11634.5427] [Topology ] . Checking for NNIs, optimizing five branches... . ( 28 sec) [ -11634.5425] [Alpha ][ 0.601587] . ( 28 sec) [ -11634.5425] [Topology ] . ( 29 sec) [ -11634.5424] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 44 sec) [ -11696.3996] [Alpha ][ 0.540948] . ( 45 sec) [ -11691.9204] [ 1351] [depth= 1] . ( 45 sec) [ -11677.2385] [ 1351] [depth= 1] . ( 46 sec) [ -11664.9913] [ 1354] [depth= 1] . ( 46 sec) [ -11640.4902] [ 1348] [depth= 4] . ( 47 sec) [ -11636.3286] [ 1349] [depth= 1] . ( 52 sec) [ -11621.4755] [Branch lengths ] . ( 52 sec) [ -11620.6479] [Alpha ][ 0.598071] . ( 62 sec) [ -11620.1700] [Branch lengths ] . ( 62 sec) [ -11620.1700] [Topology ] . ( 63 sec) [ -11620.1526] [Topology ] . ( 64 sec) [ -11620.1491] [Topology ] . ( 65 sec) [ -11620.1482] [Topology ] . ( 65 sec) [ -11620.1482] [Alpha ][ 0.598071] . ( 65 sec) [ -11620.1482] [Topology ] . ( 66 sec) [ -11620.1479] [Topology ] . ( 66 sec) [ -11620.1479] [Alpha ][ 0.598071] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -11634.542422 . Log likelihood obtained after SPR moves : -11620.147876 . Log likelihood of the current tree: -11620.147876. . Printing the most likely tree in file 'proteic_M1379_9x1557_2003.phy_phyml_tree.txt'... . Best log likelihood : -11620.147809 . Time used 0h1m16s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 265.40user 0.00system 4:35.90elapsed 96%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps