P A U P * Version 4.0a126 for Macintosh (X86) Thursday, January 24, 2013 8:02:39 PM Czech Republic Time Running on IA-32 architecture (64-bit word length) SSE vectorization enabled Multithreading enabled for likelihood using Pthreads Compiled using Intel compiler (icc) 11.1.0 (build 20091012) -----------------------------NOTICE----------------------------- This is an alpha-test version prepared for the exclusive use of course and workshop participants, as well as other authorized testers. It will expire on 1 Aug 2013. Please report bugs to david.swofford@duke.edu ---------------------------------------------------------------- Processing of file "~/Downloads/murphy29.rag1rag2.nex" begins... Data read in DNA format Data matrix has 29 taxa, 1218 characters Valid character-state symbols: ACGT Missing data identified by '?' Gaps identified by '-' "Equate" macros in effect: R,r ==> {AG} Y,y ==> {CT} M,m ==> {AC} K,k ==> {GT} S,s ==> {CG} W,w ==> {AT} H,h ==> {ACT} B,b ==> {CGT} V,v ==> {ACG} D,d ==> {AGT} N,n ==> {ACGT} Processing of input file "murphy29.rag1rag2.nex" completed. paup> GetTrees file=run1.best.all.tre; Processing TREES block from file "run1.best.all.tre": Keeping: trees from file (replacing any trees already in memory) 2 trees read from file Time used = 0.02 sec (CPU time = 0.01 sec) Note: Input trees contained branch lengths that were not stored. If you want to keep the branch lengths (at the expense of additional memory usage), you must request "storebrlens=yes" prior to getting the trees. This can be done using the "storebrlens=yes" option on the GetTrees command (or via an equivalent choice from the "More Options" subdialog of the "Get Trees" menu command), or from a "set storebrlens=yes" command within a PAUP block or from the command line. paup> lscores; Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 (HKY85 variant) Transition/transversion ratio = 2 (kappa = 3.9911424) Assumed state frequencies (empirical frequencies): A=0.26160 C=0.22842 G=0.25866 T=0.25133 These settings correspond to the HKY85 model Among-site rate variation: Assumed proportion of invariable sites = none Distribution of rates at variable sites = equal Number of distinct data patterns under this model = 551 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, tolerance=1e-07 Vector processing enabled Conditional-likelihood rescaling threshold = 1e-20 Using 2 threads on 2 processors Tree 1 2 -ln L 10856.10 10870.57 Time used to compute likelihoods = 0.05 sec (CPU time = 0.09 sec) paup> lset userbr=no rmat=est base=eq rates=gamma shape=est pinv=est; paup> lscores; Likelihood scores of tree(s) in memory: Likelihood settings: Number of substitution types = 2 Transition/transversion ratio = 2 (kappa = 4) Assumed state frequencies (set by user): A=0.25000 C=0.25000 G=0.25000 T=0.25000 These settings correspond to the K80 (=K2P)+G+I model Among-site rate variation: Assumed proportion of invariable sites = estimated Distribution of rates at variable sites = gamma (discrete approximation) Shape parameter (alpha) = estimated Number of rate categories = 4 Representation of average rate for each category = mean Number of distinct data patterns under this model = 551 Molecular clock not enforced Starting branch lengths obtained using Rogers-Swofford approximation method Branch-length optimization = one-dimensional Newton-Raphson with pass limit=20, tolerance=1e-07 Multidimensional optimizer = Praxis (tol=0.0001) Vector processing enabled Conditional-likelihood rescaling threshold = 1e-20 Using 2 threads on 2 processors Tree 1 2 ------------------------------ -ln L 9980.707 9985.238 Shape 1.242612 1.163921 P_inv 0.443534 0.438430 Time used to compute likelihoods = 22.61 sec (CPU time = 41.91 sec) paup> treedist; Symmetric difference (RF x 2) distances between trees 1 2 1 - 2 7 - Distribution of symmetric difference (RF x 2) distances between trees D normD /------------------------------------------------------------------------------------- 7 (0.135) |##################################################################################### (1) \------------------------------------------------------------------------------------- paup> contree /strict=yes majrule=yes LE50=yes; Strict consensus of 2 trees: /---------------------------------------------------------------------------------- Opossum | | /------- Sloth | /------+ | | \------- Anteater | /---------------------------------+ | | \-------------- Armadillo | | | | /---------------------------------- Mole | | | | | +---------------------------------- Free tailed bat | | | | | +---------------------------------- Flying Fox | | | | | | /------- Whale | | | /------+ | | | | \------- Hippo | /------+ | /-----+ | | | | /------+ \-------------- Pig | | | | | | | | | /------+------+ \-------------------- Llama | | | | | | | | | | | \--------------------------- Pangolin | | | | | | | | | | /-------------- Horse | | | | | | | | | | +-------------------+ /------- Rhino | | | | | \------+ | | | | | \------- Tapir | | | | | | | \------+ | /------- Cat | | | \--------------------------+ | | | \------- Caniform | /-----+ | | | | | /------- Mouse | | | | /------------+ | | | | | \------- Rat | | | | | | | | | | /------- Rabbit | | | | +------------+ | | | \--------------------+ \------- Pika | | | | | /------+ | | /------- Flying Lemur | | | | | /------+ | | | | | | \------- Strepsirrhine | | | | \-----+ | | | | \-------------- Human | | | | | /------+ | \------------------------------------------------------- Tenrecid | | | | | | | | /------- Sirenian | | | \-----------------------------------------------------+ \------+ | \------- Elephant | | | \-------------------------------------------------------------------- Sh Ear Ele Shrew | \--------------------------------------------------------------------------- Aardvark 50% Majority-rule consensus of 2 trees /------------------------------------------------------------------------------ Opossum(1) | | /------ Sloth(2) | /-100-+ | | \------ Anteater(4) | /----------------100----------------+ | | \------------ Armadillo(3) | | | | /------------------ Mole(5) | | | | | +------------------ Flying Fox(19) | | /-------50--------+ | | | | /------------ Horse(24) | | | | | | | | \-100-+ /------ Rhino(25) | | | \-100-+ | | | \------ Tapir(26) | /-100-+ | | | | /-100-+ /------------ Free tailed bat(18) | | | | | | | | | | | /-------50--------+ /------ Cat(27) | | | | | | \-100-+ | | | | | | \------ Caniform(28) | | | | | | | | | | | | /------ Whale(20) | | | | \-50--+ /-100-+ | | | | | | \------ Hippo(21) | | | | | /-100-+ | | | | | /-100-+ \------------ Pig(23) | | | | | | | | | \-100-+ \-100-+ \------------------ Llama(22) | | | | | | | \------------------------ Pangolin(29) | /-100-+ | | | | | /------ Mouse(11) | | | | /----100----+ | | | | | \------ Rat(12) | | | | | | | | | /-50--+ /------ Flying Lemur(15) | | | | | | /-100-+ | | | | | | | \------ Strepsirrhine(16) | | | \-------100-------+ \-100-+ | /-100-+ | | \------------ Human(17) | | | | | | | | | | /------ Rabbit(13) | | | | \-------100-------+ | | | | \------ Pika(14) | | | | | /-100-+ | \------------------------------------------------------ Tenrecid(6) | | | | | | | | /------ Sirenian(7) | | | \-------------------------100-------------------------+ \-----+ | \------ Elephant(8) | | | \------------------------------------------------------------------ Sh Ear Ele Shrew(9) | \------------------------------------------------------------------------ Aardvark(10) Bipartitions found in one or more trees and frequency of occurrence: 1 2 2 12345678901234567890123456789 Freq % ---------------------------------------------- ......**..................... 2 100.0% ............**............... 2 100.0% ..............**............. 2 100.0% ..............***............ 2 100.0% ..........**................. 2 100.0% ..........*******............ 2 100.0% ...................**........ 2 100.0% ...................**.*...... 2 100.0% ...................****...... 2 100.0% ...................****.....* 2 100.0% ..........................**. 2 100.0% ........................**... 2 100.0% .......................***... 2 100.0% ....*............************ 2 100.0% ....*.....******************* 2 100.0% .*.*......................... 2 100.0% .***......................... 2 100.0% .****.....******************* 2 100.0% .*****....******************* 2 100.0% .*******..******************* 2 100.0% .********.******************* 2 100.0% ..........**..***............ 1 50.0% .................*........**. 1 50.0% .................*.****...*** 1 50.0% ....*.............*....***... 1 50.0% ...................*******..* 1 50.0% .................**.......... 1 50.0% ....*............*********..* 1 50.0% paup> Log File='/Users/Brabcak/Desktop/murphy29.rag1rag2.log' start; Logging output to file "~/Desktop/murphy29.rag1rag2.log". paup> Log File='/Users/Brabcak/Desktop/murphy29.rag1rag2.log' replace; Logging of output to file "murphy29.rag1rag2.log" discontinued.