P A U P * Version 4.0a126 for Macintosh (X86) Thursday, January 24, 2013 8:49:10 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 ---------------------------------------------------------------- paup> exe ~/Downloads/murphy29.rag1rag2.nex; 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=nucboot.boot.tre; Processing TREES block from file "nucboot.boot.tre": Keeping: trees from file (replacing any trees already in memory) Maxtrees remains 100 200 trees read from file Time used = 4.52 sec (CPU time = 0.33 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> strict=no majrule=yes LE50=yes grpfreq=no; paup> contree /strict=no majrule=yes LE50=yes grpfreq=no; 50% Majority-rule consensus of 200 trees /----------------------------------------------------------------------------- Opossum(1) | | /----- Sloth(2) | /-76-+ | | \----- Anteater(4) | /-------------------98-------------------+ | | \---------- Armadillo(3) | | | | /----------------------------------------- Mole(5) | | | | | | /----- Free tailed bat(18) | | | /-----------30------------+ | | | | \----- Flying Fox(19) | | | | | | | | /----- Whale(20) | | | | /-98-+ | /-66-+ /-72-+ | | \----- Hippo(21) | | | | | /-4--+ /-38-+ | | | | | | | /-84--+ \---------- Pig(23) | | | | | | | | | | | | | | | | /-24-+ \--------------- Llama(22) | | | | | | | | | | | | | | | | | \--------------------- Pangolin(29) | | | | | | \-16-+ | | | | \-22-+ | /---------- Horse(24) | | | | | | | | | | | | \------91-------+ /----- Rhino(25) | | \-63-+ | \-96-+ | | | | \----- Tapir(26) | | | | | | | | /----- Cat(27) | | | \-------------100--------------+ | /-54--+ | \----- Caniform(28) | | | | | | | | /----- Mouse(11) | | | | /------100------+ | | | | | \----- Rat(12) | | | | | | | | \-----------61-----------+ /----- Rabbit(13) | | | | /---96----+ | | | | | \----- Pika(14) | /-32-+ | \-32--+ | | | | | /---------- Flying Lemur(15) | | | | | | | | | | \-42-+ /----- Strepsirrhine(16) | | | | \-45-+ | | | | \----- Human(17) | | | | | /-72-+ | \-------------------------------------------------------- Tenrecid(6) | | | | | | | | /----- Sirenian(7) | | | \--------------------------100---------------------------+ \----+ | \----- Elephant(8) | | | \------------------------------------------------------------------- Sh Ear Ele Shrew(9) | \------------------------------------------------------------------------ Aardvark(10) paup> Log File='/Users/Brabcak/Desktop/murphy29.rag1rag2boot.txt' start;