.......................... ooooooooooooooooooooooooooooo CURRENT SETTINGS ooooooooooooooooooooooooooooooooooo .......................... . Sequence filename : proteic_M1375_23x530_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... . 370 patterns found. (out of a total of 530 sites) . 201 sites without polymorphism (37.92%). . [Random start 1/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . This analysis requires at least 20Mo of memory space. . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10064.2029] [Alpha ][ 0.500960] . ( 1 sec) [ -10049.2119] [ 1615] [depth= 4] . ( 2 sec) [ -9788.7587] [ 1574] [depth= 9] . ( 2 sec) [ -9690.9071] [ 1568] [depth= 4] . ( 2 sec) [ -9666.4763] [ 1553] [depth= 1] . ( 2 sec) [ -9629.4811] [ 1547] [depth= 4] . ( 3 sec) [ -9595.2124] [ 1538] [depth= 1] . ( 3 sec) [ -9538.2574] [ 1522] [depth= 3] . ( 3 sec) [ -9508.9899] [ 1513] [depth= 1] . ( 4 sec) [ -9496.7877] [ 1508] [depth= 1] . ( 4 sec) [ -9489.3119] [ 1505] [depth= 1] . ( 4 sec) [ -9437.9856] [ 1497] [depth= 1] . ( 4 sec) [ -9294.1433] [ 1472] [depth= 1] . ( 5 sec) [ -9180.8705] [ 1446] [depth= 3] . ( 5 sec) [ -9047.7165] [ 1430] [depth= 8] . ( 5 sec) [ -8953.6517] [ 1430] [depth= 1] . ( 6 sec) [ -8525.4308] [ 1338] [depth= 1] . ( 6 sec) [ -8470.1527] [ 1326] [depth= 2] . ( 6 sec) [ -8430.7957] [ 1314] [depth= 7] . ( 6 sec) [ -8383.1815] [ 1303] [depth= 1] . ( 7 sec) [ -8341.8096] [ 1301] [depth= 3] . ( 7 sec) [ -8164.6356] [ 1248] [depth= 10] . ( 8 sec) [ -8137.0827] [ 1244] [depth= 2] . ( 8 sec) [ -8094.4207] [ 1239] [depth= 1] . ( 8 sec) [ -8083.2673] [ 1244] [depth= 2] . ( 9 sec) [ -8079.0095] [ 1243] [depth= 1] . ( 9 sec) [ -8074.3019] [ 1240] [depth= 1] . ( 10 sec) [ -8063.0458] [ 1237] [depth= 1] . ( 14 sec) [ -8061.8654] [ 1241] [depth= 1] . ( 15 sec) [ -8000.4010] [ 1242] [depth= 1] . ( 15 sec) [ -7996.6693] [ 1243] [depth= 1] . ( 15 sec) [ -7989.5751] [ 1242] [depth= 1] . ( 16 sec) [ -7982.5018] [ 1243] [depth= 2] . ( 16 sec) [ -7971.5577] [ 1243] [depth= 1] . ( 17 sec) [ -7965.5440] [ 1244] [depth= 2] . ( 17 sec) [ -7960.8560] [ 1244] [depth= 6] . ( 18 sec) [ -7953.5159] [ 1237] [depth= 4] . ( 19 sec) [ -7953.2287] [ 1238] [depth= 1] . ( 20 sec) [ -7889.5206] [ 1243] [depth= 6] . ( 22 sec) [ -7887.6906] [ 1243] [depth= 1] . ( 23 sec) [ -7874.7669] [ 1243] [depth= 1] . ( 23 sec) [ -7861.1033] [ 1240] [depth= 1] . ( 23 sec) [ -7833.2383] [ 1229] [depth= 2] . ( 24 sec) [ -7784.8608] [Branch lengths ] . ( 25 sec) [ -7784.3479] [Alpha ][ 0.541546] . ( 31 sec) [ -7783.6859] [ 1223] [depth= 3] . ( 32 sec) [ -7783.5736] [ 1222] [depth= 1] . ( 32 sec) [ -7783.0509] [ 1221] [depth= 1] . ( 34 sec) [ -7782.5136] [ 1221] [depth= 2] . ( 35 sec) [ -7782.1645] [ 1222] [depth= 1] . ( 45 sec) [ -7779.6361] [ 1222] [depth= 1] . ( 47 sec) [ -7778.2228] [ 1223] [depth= 1] . ( 48 sec) [ -7778.1984] [ 1224] [depth= 1] . ( 49 sec) [ -7777.8831] [ 1221] [depth= 1] . ( 49 sec) [ -7777.4871] [ 1220] [depth= 1] . ( 54 sec) [ -7775.5436] [ 1221] [depth= 1] . ( 55 sec) [ -7774.8609] [ 1221] [depth= 1] . ( 56 sec) [ -7773.3676] [ 1218] [depth= 1] . ( 59 sec) [ -7768.1137] [Branch lengths ] . ( 59 sec) [ -7768.0729] [Alpha ][ 0.553491] . ( 98 sec) [ -7767.7726] [Branch lengths ] . ( 98 sec) [ -7767.7726] [Topology ] . ( 100 sec) [ -7767.5956] [Topology ] . ( 102 sec) [ -7767.1356] [Topology ] . ( 104 sec) [ -7766.9635] [Topology ] . ( 106 sec) [ -7766.8974] [Topology ] . ( 108 sec) [ -7766.8710] [Topology ] . ( 110 sec) [ -7766.8604] [Topology ] . ( 110 sec) [ -7766.8582] [Alpha ][ 0.556420] . ( 110 sec) [ -7766.8582] [Topology ] . ( 112 sec) [ -7766.8539] [Topology ] . ( 114 sec) [ -7766.8523] [Topology ] . ( 116 sec) [ -7766.8516] [Topology ] . ( 116 sec) [ -7766.8516] [Alpha ][ 0.556420] . ( 116 sec) [ -7766.8516] [Topology ] . ( 118 sec) [ -7766.8514] [Topology ] . ( 118 sec) [ -7766.8514] [Alpha ][ 0.556420] . Checking for NNIs, optimizing five branches... . ( 133 sec) [ -7766.8493] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7766.849254. . [Random start 2/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10606.7195] [Alpha ][ 0.500960] . ( 1 sec) [ -10436.9218] [ 1595] [depth= 8] . ( 1 sec) [ -10181.3583] [ 1550] [depth= 12] . ( 2 sec) [ -9883.6886] [ 1534] [depth= 4] . ( 2 sec) [ -9767.6036] [ 1516] [depth= 1] . ( 2 sec) [ -9715.0510] [ 1507] [depth= 3] . ( 2 sec) [ -9496.4786] [ 1465] [depth= 2] . ( 3 sec) [ -9491.4284] [ 1461] [depth= 2] . ( 3 sec) [ -9417.4850] [ 1453] [depth= 2] . ( 3 sec) [ -9367.8427] [ 1452] [depth= 2] . ( 4 sec) [ -9314.2067] [ 1445] [depth= 10] . ( 4 sec) [ -9263.1365] [ 1412] [depth= 2] . ( 4 sec) [ -9128.5281] [ 1414] [depth= 1] . ( 5 sec) [ -9108.4200] [ 1408] [depth= 5] . ( 5 sec) [ -9061.8662] [ 1400] [depth= 1] . ( 5 sec) [ -8969.7527] [ 1404] [depth= 7] . ( 6 sec) [ -8943.5691] [ 1405] [depth= 1] . ( 6 sec) [ -8805.1991] [ 1406] [depth= 2] . ( 6 sec) [ -8801.7939] [ 1403] [depth= 2] . ( 6 sec) [ -8799.7488] [ 1402] [depth= 1] . ( 7 sec) [ -8796.1142] [ 1401] [depth= 2] . ( 8 sec) [ -8661.3274] [ 1396] [depth= 2] . ( 8 sec) [ -8610.9025] [ 1391] [depth= 5] . ( 8 sec) [ -8587.0818] [ 1386] [depth= 3] . ( 9 sec) [ -8580.5131] [ 1391] [depth= 1] . ( 9 sec) [ -8579.9478] [ 1390] [depth= 1] . ( 9 sec) [ -8575.2667] [ 1386] [depth= 1] . ( 10 sec) [ -8565.7513] [ 1386] [depth= 2] . ( 10 sec) [ -8565.6993] [ 1382] [depth= 7] . ( 10 sec) [ -8028.1344] [ 1251] [depth= 7] . ( 11 sec) [ -8014.2981] [ 1247] [depth= 2] . ( 11 sec) [ -8007.1963] [ 1245] [depth= 1] . ( 11 sec) [ -7998.9730] [ 1242] [depth= 1] . ( 12 sec) [ -7997.3265] [ 1243] [depth= 1] . ( 12 sec) [ -7966.9821] [ 1236] [depth= 1] . ( 13 sec) [ -7961.0879] [ 1234] [depth= 1] . ( 13 sec) [ -7951.0064] [ 1231] [depth= 1] . ( 14 sec) [ -7938.8143] [ 1233] [depth= 1] . ( 18 sec) [ -7927.1450] [ 1228] [depth= 1] . ( 20 sec) [ -7907.1936] [ 1221] [depth= 9] . ( 21 sec) [ -7864.2735] [Branch lengths ] . ( 22 sec) [ -7863.8043] [Alpha ][ 0.539416] . ( 22 sec) [ -7854.0211] [ 1217] [depth= 2] . ( 25 sec) [ -7852.4462] [ 1215] [depth= 1] . ( 34 sec) [ -7851.5317] [ 1215] [depth= 1] . ( 37 sec) [ -7851.1318] [ 1219] [depth= 1] . ( 42 sec) [ -7793.2191] [ 1221] [depth= 1] . ( 44 sec) [ -7784.6390] [ 1219] [depth= 1] . ( 48 sec) [ -7784.0009] [ 1219] [depth= 1] . ( 54 sec) [ -7781.0534] [Branch lengths ] . ( 54 sec) [ -7781.0413] [Alpha ][ 0.546109] . ( 94 sec) [ -7780.7777] [Branch lengths ] . ( 94 sec) [ -7780.7777] [Topology ] . ( 96 sec) [ -7780.7551] [Topology ] . ( 97 sec) [ -7780.7470] [Topology ] . ( 99 sec) [ -7780.7397] [Topology ] . ( 101 sec) [ -7780.7089] [Topology ] . ( 103 sec) [ -7780.4895] [Topology ] . ( 105 sec) [ -7779.0780] [Topology ] . ( 105 sec) [ -7779.0715] [Alpha ][ 0.551056] . ( 105 sec) [ -7779.0715] [Topology ] . ( 107 sec) [ -7773.6916] [Topology ] . ( 109 sec) [ -7769.4966] [Topology ] . ( 111 sec) [ -7768.7359] [Topology ] . ( 113 sec) [ -7768.6077] [Topology ] . ( 115 sec) [ -7768.5855] [Topology ] . ( 116 sec) [ -7768.5813] [Topology ] . ( 117 sec) [ -7768.5774] [Alpha ][ 0.554890] . ( 117 sec) [ -7768.5774] [Topology ] . ( 119 sec) [ -7768.5767] [Topology ] . ( 119 sec) [ -7768.5767] [Alpha ][ 0.554890] . Checking for NNIs, optimizing five branches... . ( 134 sec) [ -7768.2497] [Topology ] . Checking for NNIs, optimizing five branches... . ( 148 sec) [ -7767.7660] [Topology ] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7767.766029. . [Random start 3/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 0 sec) [ -10326.7125] [Alpha ][ 0.500960] . ( 1 sec) [ -10079.6395] [ 1634] [depth= 7] . ( 1 sec) [ -9761.5828] [ 1517] [depth= 6] . ( 1 sec) [ -9347.8415] [ 1509] [depth= 2] . ( 2 sec) [ -9256.4228] [ 1467] [depth= 1] . ( 2 sec) [ -9240.0818] [ 1454] [depth= 1] . ( 2 sec) [ -9179.4898] [ 1450] [depth= 1] . ( 3 sec) [ -9136.7900] [ 1446] [depth= 1] . ( 3 sec) [ -8940.1925] [ 1414] [depth= 6] . ( 3 sec) [ -8887.7508] [ 1416] [depth= 1] . ( 3 sec) [ -8827.2655] [ 1405] [depth= 5] . ( 4 sec) [ -8774.5315] [ 1393] [depth= 1] . ( 4 sec) [ -8754.9718] [ 1381] [depth= 2] . ( 4 sec) [ -8728.7892] [ 1382] [depth= 1] . ( 5 sec) [ -8709.7848] [ 1372] [depth= 1] . ( 5 sec) [ -8706.9347] [ 1372] [depth= 1] . ( 5 sec) [ -8643.8123] [ 1372] [depth= 1] . ( 5 sec) [ -8623.5129] [ 1369] [depth= 2] . ( 6 sec) [ -8550.2140] [ 1362] [depth= 3] . ( 6 sec) [ -8515.9302] [ 1354] [depth= 1] . ( 6 sec) [ -8442.0643] [ 1323] [depth= 1] . ( 7 sec) [ -8438.5816] [ 1323] [depth= 3] . ( 7 sec) [ -8373.1928] [ 1311] [depth= 1] . ( 7 sec) [ -8360.5311] [ 1312] [depth= 1] . ( 7 sec) [ -8336.5009] [ 1311] [depth= 4] . ( 8 sec) [ -8280.7367] [ 1296] [depth= 2] . ( 8 sec) [ -8245.9098] [ 1284] [depth= 1] . ( 8 sec) [ -8245.7545] [ 1282] [depth= 4] . ( 9 sec) [ -8233.5747] [ 1280] [depth= 3] . ( 9 sec) [ -8229.1017] [ 1276] [depth= 4] . ( 9 sec) [ -8200.4748] [ 1276] [depth= 1] . ( 10 sec) [ -8195.9635] [ 1275] [depth= 3] . ( 10 sec) [ -8189.7384] [ 1275] [depth= 1] . ( 10 sec) [ -8183.2868] [ 1275] [depth= 1] . ( 10 sec) [ -8163.4225] [ 1268] [depth= 11] . ( 11 sec) [ -8138.4808] [ 1261] [depth= 1] . ( 11 sec) [ -8124.9779] [ 1259] [depth= 1] . ( 12 sec) [ -8083.1866] [ 1246] [depth= 4] . ( 13 sec) [ -7964.5906] [ 1228] [depth= 1] . ( 14 sec) [ -7897.4619] [ 1218] [depth= 1] . ( 14 sec) [ -7887.1693] [ 1219] [depth= 1] . ( 15 sec) [ -7885.4336] [ 1218] [depth= 1] . ( 16 sec) [ -7881.5663] [ 1217] [depth= 1] . ( 17 sec) [ -7879.4263] [ 1221] [depth= 1] . ( 18 sec) [ -7796.4870] [Branch lengths ] . ( 18 sec) [ -7795.0647] [Alpha ][ 0.568322] . ( 19 sec) [ -7791.4474] [ 1220] [depth= 2] . ( 19 sec) [ -7790.7903] [ 1223] [depth= 4] . ( 21 sec) [ -7788.1685] [ 1220] [depth= 1] . ( 22 sec) [ -7786.6359] [ 1218] [depth= 1] . ( 23 sec) [ -7785.8425] [ 1222] [depth= 2] . ( 26 sec) [ -7785.2066] [ 1219] [depth= 1] . ( 30 sec) [ -7784.1050] [ 1218] [depth= 1] . ( 31 sec) [ -7783.4369] [ 1218] [depth= 1] . ( 41 sec) [ -7781.7012] [ 1218] [depth= 1] . ( 47 sec) [ -7781.1782] [ 1221] [depth= 1] . ( 53 sec) [ -7774.5646] [Branch lengths ] . ( 53 sec) [ -7774.5631] [Alpha ][ 0.565853] . ( 53 sec) [ -7772.5399] [ 1219] [depth= 1] . ( 55 sec) [ -7771.8143] [ 1216] [depth= 1] . ( 81 sec) [ -7771.4620] [ 1215] [depth= 2] . ( 84 sec) [ -7768.4000] [Branch lengths ] . ( 84 sec) [ -7768.3913] [Alpha ][ 0.559852] . ( 85 sec) [ -7767.5911] [ 1218] [depth= 2] . ( 119 sec) [ -7766.9228] [Branch lengths ] . ( 120 sec) [ -7766.9227] [Alpha ][ 0.559192] . ( 159 sec) [ -7766.8611] [Branch lengths ] . ( 159 sec) [ -7766.8611] [Topology ] . ( 161 sec) [ -7766.8560] [Topology ] . ( 163 sec) [ -7766.8542] [Topology ] . ( 165 sec) [ -7766.8535] [Topology ] . ( 165 sec) [ -7766.8524] [Alpha ][ 0.557022] . ( 165 sec) [ -7766.8524] [Topology ] . ( 167 sec) [ -7766.8518] [Topology ] . ( 167 sec) [ -7766.8518] [Alpha ][ 0.557022] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7766.851755. . [Random start 4/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10114.3615] [Alpha ][ 0.500960] . ( 1 sec) [ -10078.6840] [ 1591] [depth= 5] . ( 2 sec) [ -9806.3445] [ 1479] [depth= 6] . ( 2 sec) [ -9681.0729] [ 1476] [depth= 1] . ( 2 sec) [ -9281.2604] [ 1472] [depth= 4] . ( 2 sec) [ -9278.3645] [ 1465] [depth= 3] . ( 3 sec) [ -9261.7951] [ 1466] [depth= 1] . ( 3 sec) [ -9247.6951] [ 1467] [depth= 2] . ( 4 sec) [ -9226.9080] [ 1467] [depth= 2] . ( 4 sec) [ -9041.3898] [ 1466] [depth= 4] . ( 4 sec) [ -8985.9056] [ 1447] [depth= 5] . ( 5 sec) [ -8965.0965] [ 1445] [depth= 1] . ( 5 sec) [ -8918.7960] [ 1412] [depth= 6] . ( 5 sec) [ -8911.3557] [ 1410] [depth= 2] . ( 5 sec) [ -8827.8395] [ 1393] [depth= 6] . ( 6 sec) [ -8806.7849] [ 1388] [depth= 2] . ( 6 sec) [ -8747.3814] [ 1383] [depth= 3] . ( 6 sec) [ -8550.2721] [ 1375] [depth= 2] . ( 7 sec) [ -8403.7472] [ 1346] [depth= 5] . ( 7 sec) [ -8320.2945] [ 1299] [depth= 1] . ( 7 sec) [ -8312.5634] [ 1300] [depth= 6] . ( 8 sec) [ -8287.4201] [ 1292] [depth= 1] . ( 8 sec) [ -8284.3491] [ 1291] [depth= 1] . ( 8 sec) [ -8269.6679] [ 1285] [depth= 3] . ( 9 sec) [ -8251.5949] [ 1286] [depth= 3] . ( 9 sec) [ -8235.9858] [ 1282] [depth= 1] . ( 9 sec) [ -8221.5768] [ 1278] [depth= 1] . ( 10 sec) [ -8155.3277] [ 1276] [depth= 3] . ( 10 sec) [ -8149.9474] [ 1278] [depth= 3] . ( 11 sec) [ -8143.5581] [ 1280] [depth= 1] . ( 11 sec) [ -8143.1998] [ 1278] [depth= 1] . ( 13 sec) [ -8082.7797] [ 1293] [depth= 2] . ( 14 sec) [ -8077.8045] [ 1282] [depth= 2] . ( 14 sec) [ -8077.5283] [ 1282] [depth= 1] . ( 15 sec) [ -8066.6467] [ 1282] [depth= 1] . ( 15 sec) [ -7929.2641] [ 1236] [depth= 1] . ( 16 sec) [ -7926.4591] [ 1235] [depth= 1] . ( 17 sec) [ -7919.7090] [ 1235] [depth= 1] . ( 17 sec) [ -7909.2278] [ 1231] [depth= 2] . ( 18 sec) [ -7893.0399] [ 1225] [depth= 3] . ( 19 sec) [ -7888.0839] [ 1222] [depth= 1] . ( 19 sec) [ -7878.2829] [ 1220] [depth= 1] . ( 20 sec) [ -7817.4549] [Branch lengths ] . ( 20 sec) [ -7816.5918] [Alpha ][ 0.553030] . ( 26 sec) [ -7815.6104] [ 1221] [depth= 1] . ( 27 sec) [ -7814.9755] [ 1221] [depth= 1] . ( 28 sec) [ -7808.9918] [ 1221] [depth= 1] . ( 33 sec) [ -7807.4378] [ 1224] [depth= 2] . ( 34 sec) [ -7805.1802] [ 1224] [depth= 1] . ( 39 sec) [ -7803.4996] [ 1227] [depth= 1] . ( 40 sec) [ -7801.1368] [ 1225] [depth= 1] . ( 40 sec) [ -7787.9647] [ 1223] [depth= 7] . ( 40 sec) [ -7786.8311] [ 1218] [depth= 2] . ( 49 sec) [ -7785.9439] [ 1218] [depth= 1] . ( 50 sec) [ -7784.8662] [ 1221] [depth= 1] . ( 54 sec) [ -7774.9106] [Branch lengths ] . ( 54 sec) [ -7774.8781] [Alpha ][ 0.564245] . ( 54 sec) [ -7772.6994] [ 1219] [depth= 1] . ( 75 sec) [ -7771.9150] [ 1216] [depth= 1] . ( 76 sec) [ -7771.2955] [ 1220] [depth= 1] . ( 88 sec) [ -7769.8511] [Branch lengths ] . ( 88 sec) [ -7769.8449] [Alpha ][ 0.559210] . ( 130 sec) [ -7769.7286] [Branch lengths ] . ( 130 sec) [ -7769.7286] [Topology ] . ( 132 sec) [ -7769.7153] [Topology ] . ( 134 sec) [ -7769.7109] [Topology ] . ( 135 sec) [ -7769.7090] [Topology ] . ( 137 sec) [ -7769.7080] [Topology ] . ( 138 sec) [ -7769.7067] [Alpha ][ 0.556879] . ( 138 sec) [ -7769.7067] [Topology ] . ( 140 sec) [ -7769.7059] [Topology ] . ( 140 sec) [ -7769.7059] [Alpha ][ 0.556879] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7769.705938. . [Random start 5/ 5] . Computing pairwise distances... . Building BioNJ tree... . Randomising the tree... . Maximizing likelihood (using SPR moves)... . ( 1 sec) [ -10182.3009] [Alpha ][ 0.500960] . ( 1 sec) [ -10159.1709] [ 1602] [depth= 5] . ( 1 sec) [ -9982.2534] [ 1570] [depth= 7] . ( 2 sec) [ -9941.9737] [ 1557] [depth= 2] . ( 2 sec) [ -9805.6902] [ 1527] [depth= 6] . ( 3 sec) [ -9787.8982] [ 1516] [depth= 6] . ( 3 sec) [ -9703.8132] [ 1501] [depth= 3] . ( 4 sec) [ -9505.6315] [ 1467] [depth= 3] . ( 4 sec) [ -9000.0318] [ 1364] [depth= 1] . ( 5 sec) [ -8925.8873] [ 1357] [depth= 7] . ( 5 sec) [ -8812.7671] [ 1355] [depth= 1] . ( 5 sec) [ -8758.5301] [ 1353] [depth= 4] . ( 5 sec) [ -8627.8138] [ 1353] [depth= 1] . ( 6 sec) [ -8613.3550] [ 1353] [depth= 1] . ( 6 sec) [ -8593.0077] [ 1352] [depth= 9] . ( 6 sec) [ -8569.8603] [ 1353] [depth= 1] . ( 6 sec) [ -8566.8207] [ 1355] [depth= 1] . ( 7 sec) [ -8562.0109] [ 1354] [depth= 5] . ( 7 sec) [ -8542.7249] [ 1352] [depth= 1] . ( 7 sec) [ -8497.6345] [ 1353] [depth= 9] . ( 8 sec) [ -8409.4559] [ 1351] [depth= 2] . ( 9 sec) [ -8383.9368] [ 1348] [depth= 2] . ( 9 sec) [ -8316.5278] [ 1342] [depth= 7] . ( 11 sec) [ -8263.6329] [ 1319] [depth= 2] . ( 13 sec) [ -8209.4228] [ 1294] [depth= 1] . ( 13 sec) [ -8182.9525] [ 1287] [depth= 4] . ( 13 sec) [ -8154.8827] [ 1284] [depth= 1] . ( 14 sec) [ -8094.2281] [ 1276] [depth= 2] . ( 15 sec) [ -8080.5821] [ 1273] [depth= 1] . ( 18 sec) [ -8079.9522] [ 1274] [depth= 1] . ( 18 sec) [ -8060.5926] [ 1270] [depth= 2] . ( 19 sec) [ -7925.2626] [ 1232] [depth= 2] . ( 19 sec) [ -7914.2071] [ 1231] [depth= 1] . ( 20 sec) [ -7868.1823] [ 1224] [depth= 1] . ( 21 sec) [ -7867.3217] [ 1227] [depth= 1] . ( 22 sec) [ -7862.0666] [ 1222] [depth= 2] . ( 22 sec) [ -7826.6152] [Branch lengths ] . ( 23 sec) [ -7826.3641] [Alpha ][ 0.529036] . ( 23 sec) [ -7822.9529] [ 1222] [depth= 1] . ( 24 sec) [ -7821.2142] [ 1220] [depth= 1] . ( 25 sec) [ -7818.7647] [ 1220] [depth= 4] . ( 29 sec) [ -7817.2298] [ 1221] [depth= 1] . ( 29 sec) [ -7810.5563] [ 1221] [depth= 2] . ( 31 sec) [ -7809.8483] [ 1226] [depth= 1] . ( 32 sec) [ -7806.8625] [ 1222] [depth= 1] . ( 32 sec) [ -7804.5515] [ 1222] [depth= 1] . ( 47 sec) [ -7804.3820] [ 1222] [depth= 1] . ( 47 sec) [ -7803.6484] [ 1222] [depth= 1] . ( 53 sec) [ -7797.1237] [Branch lengths ] . ( 54 sec) [ -7797.0417] [Alpha ][ 0.545665] . ( 103 sec) [ -7796.6264] [Branch lengths ] . ( 103 sec) [ -7796.6264] [Topology ] . ( 105 sec) [ -7796.5895] [Topology ] . ( 107 sec) [ -7796.5743] [Topology ] . ( 109 sec) [ -7796.5533] [Topology ] . ( 111 sec) [ -7796.4399] [Topology ] . ( 112 sec) [ -7795.6599] [Topology ] . ( 114 sec) [ -7791.6504] [Topology ] . ( 115 sec) [ -7791.6396] [Alpha ][ 0.551980] . ( 115 sec) [ -7791.6396] [Topology ] . ( 117 sec) [ -7780.1931] [Topology ] . ( 118 sec) [ -7772.8278] [Topology ] . ( 120 sec) [ -7771.1047] [Topology ] . ( 122 sec) [ -7770.2218] [Topology ] . ( 124 sec) [ -7769.7884] [Topology ] . ( 126 sec) [ -7769.7281] [Topology ] . ( 128 sec) [ -7769.7155] [Topology ] . ( 130 sec) [ -7769.7122] [Topology ] . ( 131 sec) [ -7769.7111] [Topology ] . ( 133 sec) [ -7769.7052] [Alpha ][ 0.556525] . ( 133 sec) [ -7769.7052] [Topology ] . ( 135 sec) [ -7769.7051] [Topology ] . ( 136 sec) [ -7769.7051] [Alpha ][ 0.556525] . Checking for NNIs, optimizing five branches... . Log likelihood of the current tree: -7769.705135. . Computing pairwise distances... . Building BioNJ tree... . Maximizing likelihood (using NNI moves)... . ( 1 sec) [ -7895.0956] [Alpha ][ 0.500960] . ( 1 sec) [ -7895.0956] [Topology ] . ( 2 sec) [ -7829.5107] [Topology ] . ( 4 sec) [ -7808.3573] [Topology ] . ( 6 sec) [ -7794.6964] [Topology ] . ( 8 sec) [ -7792.1340] [Topology ] . ( 10 sec) [ -7791.3984] [Topology ] . ( 12 sec) [ -7791.0973] [Topology ] . ( 14 sec) [ -7790.9340] [Topology ] . ( 16 sec) [ -7790.8350] [Topology ] . ( 17 sec) [ -7790.7717] [Topology ] . Checking for NNIs, optimizing five branches... . ( 35 sec) [ -7790.6235] [Topology ] . ( 35 sec) [ -7789.9131] [Alpha ][ 0.549460] . ( 35 sec) [ -7789.9131] [Topology ] . ( 37 sec) [ -7789.8572] [Topology ] . ( 39 sec) [ -7789.8349] [Topology ] . ( 41 sec) [ -7789.8245] [Topology ] . ( 43 sec) [ -7789.8194] [Topology ] . ( 45 sec) [ -7789.8169] [Topology ] . ( 47 sec) [ -7789.8156] [Topology ] . Checking for NNIs, optimizing five branches... . ( 62 sec) [ -7789.8077] [Alpha ][ 0.554972] . ( 62 sec) [ -7789.8077] [Topology ] . ( 64 sec) [ -7789.8057] [Topology ] . ( 66 sec) [ -7789.8048] [Topology ] . Checking for NNIs, optimizing five branches... . ( 81 sec) [ -7789.8047] [Alpha ][ 0.555527] . ( 81 sec) [ -7789.8047] [Topology ] . ( 83 sec) [ -7789.8041] [Topology ] . Checking for NNIs, optimizing five branches... . Checking for NNIs, optimizing five branches... . Maximizing likelihood (using SPR moves)... . ( 113 sec) [ -7895.0956] [Alpha ][ 0.500960] . ( 114 sec) [ -7872.7451] [ 1229] [depth= 6] . ( 114 sec) [ -7865.3784] [ 1228] [depth= 1] . ( 115 sec) [ -7858.7954] [ 1233] [depth= 1] . ( 116 sec) [ -7857.8381] [ 1228] [depth= 5] . ( 116 sec) [ -7840.8906] [ 1223] [depth= 1] . ( 118 sec) [ -7830.0349] [ 1223] [depth= 1] . ( 120 sec) [ -7823.2777] [ 1222] [depth= 1] . ( 121 sec) [ -7821.3573] [ 1221] [depth= 2] . ( 121 sec) [ -7816.3418] [ 1220] [depth= 2] . ( 122 sec) [ -7815.2907] [ 1221] [depth= 4] . ( 125 sec) [ -7814.7194] [ 1221] [depth= 1] . ( 126 sec) [ -7810.1359] [ 1221] [depth= 1] . ( 129 sec) [ -7809.7535] [ 1222] [depth= 1] . ( 129 sec) [ -7806.7649] [ 1221] [depth= 1] . ( 130 sec) [ -7803.3865] [ 1222] [depth= 1] . ( 133 sec) [ -7799.6012] [ 1217] [depth= 1] . ( 135 sec) [ -7797.8988] [ 1216] [depth= 1] . ( 137 sec) [ -7795.6989] [ 1218] [depth= 1] . ( 141 sec) [ -7772.8183] [Branch lengths ] . ( 141 sec) [ -7772.3425] [Alpha ][ 0.540654] . ( 143 sec) [ -7771.1929] [ 1218] [depth= 1] . ( 143 sec) [ -7769.4845] [ 1215] [depth= 1] . ( 175 sec) [ -7767.9935] [Branch lengths ] . ( 176 sec) [ -7767.9634] [Alpha ][ 0.551374] . ( 178 sec) [ -7767.4538] [ 1216] [depth= 3] . ( 207 sec) [ -7766.8638] [Branch lengths ] . ( 207 sec) [ -7766.8595] [Alpha ][ 0.555429] . ( 242 sec) [ -7766.8126] [Branch lengths ] . ( 242 sec) [ -7766.8126] [Topology ] . ( 244 sec) [ -7766.8083] [Topology ] . ( 246 sec) [ -7766.8067] [Topology ] . ( 248 sec) [ -7766.8060] [Topology ] . ( 248 sec) [ -7766.8055] [Alpha ][ 0.556785] . ( 248 sec) [ -7766.8055] [Topology ] . ( 250 sec) [ -7766.8050] [Topology ] . ( 250 sec) [ -7766.8050] [Alpha ][ 0.556785] . Checking for NNIs, optimizing five branches... . Log likelihood obtained after NNI moves : -7789.804126 . Log likelihood obtained after SPR moves : -7766.804982 . Log likelihood of the current tree: -7766.804982. . Printing the most likely tree in file 'proteic_M1375_23x530_2003.phy_phyml_tree.txt'... . Best log likelihood : -7766.804982 . Time used 0h4m26s oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo 1056.05user 0.00system 17:50.99elapsed 98%CPU (0avgtext+0avgdata 0maxresident)k 0inputs+0outputs (0major+0minor)pagefaults 0swaps