fastDNAml, version 1.2.2, January 3, 2000, Copyright (C) 1998, 1999, 2000 by Gary J. Olsen Based in part on Joseph Felsenstein's Nucleic acid sequence Maximum Likelihood method, version 3.3 9 Species, 88 Sites Quick add (only local branches initially optimized) in effect Rearrangements of partial trees may cross 1 branch. Rearrangements of full tree may cross 1 branch. Name Sequences ---- --------- LYS ---------G GGTCGTTAGC TCAGTTGGT- AGAGCAGTTG ACTTTTAATC AATTGGTCGC MET .......... .C.ACG.... .........T ......CA.C ...CA....G .TGG....A. ASP .......... .AG..G...T .....C...T ...AT.CC.. C..G.C.CG. .GGG...... ALA .......... ..GGCA.... ....C...G. .....GCC.. CT..GC.CG. .GGA....TG GLY .......... C.GGCG...T ...A-..... ...A.GAGA. CT.CCC..G. TC.ATA-..A CYS .......... .CG.....A. AA..-C.... TAT.T..CG. .T.GCA.... CG.CTAGTC. PHE .......... CCCG.A.... .....C.... .......GG. .T.GAA.... CCCGT...CT LEU GCGAAGGTG. C.GAA..G.T AG.CGC.C.. ..CTTCAGGT GT.AG.GTC. TTAC..A..T GLU .......... TCC.C..C.T CT..AG.CCC ..GA..CCGC C....C.--- CGGC...AA. LYS A--GGTTCGA ATCCTGCACG ACCCACCA MET .......... ....C.TCGT .G...... ASP G......... G...C.TC.. TT..G... ALA C......... TC..GCGCGC T....... GLY G......... T...CTTCGC C.G.T... CYS -......... C...G.A... CG..T... PHE T......... T...GAGT.C GGG..... LEU GGG.....A. G...CC.C.C T.G..... GLU .GG....... ....CCTGG. GGA.G... Total weight of positions in analysis = 88 There are 68 distinct data patterns (columns) Empirical Base Frequencies: A 0.19048 C 0.28860 G 0.30447 T(U) 0.21645 Transition/transversion ratio = 2.000000 (Transition/transversion parameter = 1.575553) Adding species: LYS MET ASP ALA Tested 3 alternative trees Ln Likelihood = -320.37492 GLY Tested 5 alternative trees Ln Likelihood = -396.54054 Doing local rearrangements Tested 4 alternative trees CYS Tested 7 alternative trees Ln Likelihood = -482.04000 Doing local rearrangements Tested 6 alternative trees PHE Tested 9 alternative trees Ln Likelihood = -559.43928 Doing local rearrangements Tested 8 alternative trees LEU Tested 11 alternative trees Ln Likelihood = -668.06379 Doing local rearrangements Tested 10 alternative trees GLU Tested 13 alternative trees Ln Likelihood = -750.94310 Doing local rearrangements Tested 12 alternative trees Examined 89 trees +---------- PHE +------------5 ! +---------- CYS ! ---4 +-------------------- GLU ! +--7 ! ! +--- MET ! ! +-----1 +------------------------------- LEU ! ! +--------6 ! ! +------3 +--- GLY ! ! ! ! ! +-----2 +------- ALA ! ! ! +---- ASP ! + LYS Remember: this is an unrooted tree! Ln Likelihood = -750.94310 Between And Length Approx. Confidence Limits ------- --- ------ ------- ---------- ------ 4 5 0.34227 ( 0.15913, 0.61093) ** 5 PHE 0.29107 ( 0.12244, 0.52938) ** 5 CYS 0.30664 ( 0.13342, 0.55430) ** 4 1 0.15648 ( 0.04183, 0.29937) ** 1 7 0.07850 ( zero, 0.19408) * 7 GLU 0.54833 ( 0.32240, 0.92245) ** 7 MET 0.12155 ( 0.01672, 0.24948) ** 1 2 0.16328 ( 0.03719, 0.32445) ** 2 3 0.17867 ( 0.03840, 0.36382) ** 3 6 0.25646 ( 0.08153, 0.50767) ** 6 LEU 0.84028 ( 0.51440, 1.64754) ** 6 GLY 0.11717 ( zero, 0.31316) 3 ALA 0.19492 ( 0.05856, 0.37330) ** 2 ASP 0.12896 ( 0.01663, 0.26827) ** 4 LYS 0.00513 ( zero, 0.11242) * = significantly positive, P < 0.05 ** = significantly positive, P < 0.01 Tree also written to treefile.360119