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wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 0.38| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 1.09| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 0.33| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 0.54| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 0.23| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 0.20| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 0.10| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 3.87| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 0.42| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 0.40| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 973--973 []|\OT1/cmr/m/n/6 0.13| 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[]|\OT1/cmr/m/n/6 5.81| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 8.33| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 2.44| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 4.85| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 8.62| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 6.20| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 1.95| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 3.84| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 4.58| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 6.95| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 6.10| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 1.44| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--976 []|\OT1/cmr/m/n/6 3.53| [] Overfull \hbox (3.72147pt too wide) in paragraph at lines 976--977 []|\OT1/cmr/m/n/6 7.09| [] Overfull \hbox (37.789pt too wide) in paragraph at lines 953--979 [] [] [25] Underfull \hbox (badness 10000) in paragraph at lines 1020--1021 [] Overfull \hbox (6.4885pt too wide) in paragraph at lines 1022--1033 [] [] [26] [27] [28] [29] [30] Overfull \hbox (39.8485pt too wide) in alignment at lines 1227--1233 [][][] [] [] [31] Underfull \hbox (badness 1968) in paragraph at lines 1246--1250 \OT1/cmr/m/n/12 po-nents of a mix-ture are in-de-pen-dant. In other words, we h ave [] [32] [33] [34] Underfull \hbox (badness 2189) in paragraph at lines 1402--1402 []\OT1/cmr/bx/n/14.4 Setting up mix-ture and par-ti-tion mod-els in [] [35] [36] [37] Underfull \hbox (badness 1430) in paragraph at lines 1552--1554 []\OT1/cmtt/m/n/12 optimise.tree="yes"|"true"|"no"|"false"\OT1/cmr/m/n/12 . The start-ing tree [] [38] Overfull \hbox (9.87488pt too wide) in paragraph at lines 1571--1574 []\OT1/cmtt/m/n/12 model="JC69"|"K80"|"F81"|"F84"|"HKY85"|"TN93"|"GTR"|"custom" [] Overfull \hbox (65.4499pt too wide) in paragraph at lines 1571--1574 \OT1/cmtt/m/n/12 model="LG"|"WAG"|"JTT"|"MtREV"|"Dayhoff"|"DCMut"|"RtREV"|"CpRE V"|"VT" [] Underfull \hbox (badness 10000) in paragraph at lines 1571--1574 \OT1/cmtt/m/n/12 |"Blosum62"|"MtMam"|"MtArt"|"HIVw"|"HIVb"|"customaa" \OT1/cmr/ m/n/12 for [] Underfull \hbox (badness 1077) in paragraph at lines 1578--1582 []\OT1/cmtt/m/n/12 ratematrix.code="filename"\OT1/cmr/m/n/12 . When used in con -junc-tion with [] Underfull \hbox (badness 10000) in paragraph at lines 1590--1593 []\OT1/cmr/m/n/12 The \OT1/cmtt/m/n/12 ratematrices \OT1/cmr/m/n/12 com-po-nent has the at-tribute [] [39] Underfull \hbox (badness 10000) in paragraph at lines 1614--1616 []\OT1/cmtt/m/n/12 optimise.freqs="true|yes|false|no"\OT1/cmr/m/n/12 . Nu-cleot ide fre-quen- [] Underfull \hbox (badness 10000) in paragraph at lines 1614--1616 \OT1/cmr/m/n/12 cies can be op-ti-mised so as to max-imise the like-li-hood [] [40] [41] [42] Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 1757. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `\Gamma' on input line 1757. Package hyperref Warning: Token not allowed in a PDF string (PDFDocEncoding): (hyperref) removing `math shift' on input line 1757. [43] [44] [45] Underfull \hbox (badness 7012) in paragraph at lines 1904--1908 []\OT1/cmr/m/n/12 In or-der to fit the LG4X model to the \OT1/cmtt/m/n/12 prote ic \OT1/cmr/m/n/12 se-quence [] Underfull \hbox (badness 8056) in paragraph at lines 1904--1908 \OT1/cmr/m/n/12 file pro-vided in the \OT1/cmtt/m/n/12 examples/ \OT1/cmr/m/n/1 2 di-rec-tory, sim-ply type \OT1/cmtt/m/n/12 ./phyml [] [46] [47] [48] [49] Underfull \hbox (badness 2126) in paragraph at lines 2064--2067 []\OT1/cmr/m/n/12 It re-lies on a Gibbs sam-pler which out-per-forms the ``stan -dard'' [] [50] [51] [52] [53] Underfull \hbox (badness 1648) in paragraph at lines 2245--2257 \OT1/cmr/m/n/12 The pro-gram Phy-Time gen-er-ates two out-put files. The file c alled [] [54] [55] [56] [57] [58] [59] Underfull \hbox (badness 10000) in paragraph at lines 2477--2478 [] Underfull \hbox (badness 10000) in paragraph at lines 2484--2485 [] Underfull \hbox (badness 10000) in paragraph at lines 2489--2490 [] Underfull \hbox (badness 10000) in paragraph at lines 2494--2495 [] [60] Underfull \hbox (badness 10000) in paragraph at lines 2499--2500 [] (./phyml-manual.bbl [61] [62] [63] [64]) (./phyml-manual.ind [65] [66 ] [67]) Package atveryend Info: Empty hook `BeforeClearDocument' on input line 2519. Package atveryend Info: Empty hook `AfterLastShipout' on input line 2519. (./phyml-manual.aux) Package atveryend Info: Executing hook `AtVeryEndDocument' on input line 2519. Package atveryend Info: Executing hook `AtEndAfterFileList' on input line 2519. Package rerunfilecheck Info: File `phyml-manual.out' has not changed. (rerunfilecheck) Checksum: F1FACC1F2BF38B420E074BA89143FA06;4765. Package atveryend Info: Empty hook `AtVeryVeryEnd' on input line 2519. ) Here is how much of TeX's memory you used: 7676 strings out of 495059 111248 string characters out of 3182030 269600 words of memory out of 3000000 10574 multiletter control sequences out of 15000+200000 12459 words of font info for 46 fonts, out of 3000000 for 9000 14 hyphenation exceptions out of 8191 36i,11n,38p,273b,530s stack positions out of 5000i,500n,10000p,200000b,50000s Output written on phyml-manual.pdf (67 pages, 397031 bytes). PDF statistics: 1032 PDF objects out of 1200 (max. 8388607) 935 compressed objects within 10 object streams 207 named destinations out of 1000 (max. 500000) 505 words of extra memory for PDF output out of 10000 (max. 10000000)