#NEXUS [This file contains a simulated DNA data set followed by a PAUP block with instructions to conduct a likelihood analysis. The following numbered list corresponds with the numbered lines in the PAUP block. (1) Construct a Neighbor Joining tree. (2) Compute the likelihood of the NJ tree assuming the HKY85 model of sequence evolution (Hasegawa, M., Kishino, H., and Yano, T., 1985) with gamma distributed rates (Yang, 1994), where the transition/transversion rate ratio and the shape parameter of the gamma distribution are estimated from the data and empirical base frequencies are used. (3) Change the optimality criterion to maximum likelihood. (4) Set the parameter values to those that were estimated on the neighbor joining tree. (5) Conduct a heuristic search with five random addition sequences and TBR branch swapping. ] Begin taxa; Dimensions ntax=8; taxlabels A B C D E F G H ; end; Begin characters; Dimensions nchar=200; Format datatype=dna interleave; Matrix A CGAATATAACGGAGCCAGTACTCAGACGCACTGCCAACCCAGCGAAGCCCGATACGCCGT B CGAATATAACGAAGCCAGTATTCAGACGCACTGCTAACCCAGCGGAGCCCGGTACGCCGT C CGAATATAACAAAGCCAGTACTCGGACGCACTACCAACCCAGCGGAGCCCGATACGCCAT D CGAATACAACAAAGCCAGTATTCAGACGCACTGCCAACCCAACAGAGACCGGCGTGCTAT E CGAATACAACAAAGCCAGTATTCAGACGCACTGCCAACCCAGCAGAGACCCCCACGCTAT F CGAATACAACAAAGCCAGTATTCAGACGCACTGCCAACCCAGCAGAGACCCACACGCTAT G CGAATACAACAAAGCCAATATTCAGACGGACTGCCAACCCAGCAGAGACCGACACGTCAT H CGAATACAACAAAGCCAATATTCAGACGGACTGCCAACCCGGCAGAGACCGACGCGTCAT A CGCATGAACGCTCTCCGCATGCAAAGTCCAACAAGTCAAACGGGATTCGGATCGTGCACG B TGCGTGGACGTTCCTCGCTCACAAGGTCGAGCAGTTCAAACGAGGATTGGAGCGTACAAC C AAGATGCACATTTTCCGTAGATAAAACCGAAACATTCAAGCGAATGCTACACCTAACGGC D AAAATGTATAACTTCCGTGCACAAAACCAAAAAACCCAAGCGGACAATAAGATACGCGGC E AACACACACGACGCCCGTAAACAAAACTAAAAAAGCCGACCAGGCGTACGAGGACAGAAT F AAGATACATGATACCCGGGCACAAAACCAGAAAAGCCGACCGAATGTGTAAGCGCCAAGT G AAAACACATTAATGCCGTACACAGGACCAAAACATTCAAAAGGAACGGTAGCTATAACAA H AAAATACATGATTCCCGTACACAAAATCACAAAATCCAAACGAAGGAGTTAATACGGAAC A AATGGTGATTGCGAACTCAAGTCAAGCACAACTCTGAGCATTCCTGAAACTACTGGAGAC B AATGCCCAACATCACTTCCACTAAAACCCCGCTCTGCACCGCACGACAGAACGACACTGA C GGGGTTAGTCGAAAGACTATCCAGAACGGAATTACCTGGATCGCTAGGACAAAACAGAGG D GAATGATACCTAAGAACCGCGCGGACTAATAAGACACGCTCTGATGCAGGCCTGCCGAAA E ACACTATGCGTCATGAAAGTCTGCTCCGACAGGATTTGTCTTACGCGTTCTCACCTATAG F GAAGACTGCGCCACCGACATCTGATGCACCACTGTCTGTACAGCGCCAGCGGAATACGGC G AGCCATCGCCTAAGTAAAGCCCAGCACAGTATGTGCCGTCCTTCTCATATAACTCTCACG H AGGCAGCACTTGGGCCTGGCTTAGAATGTCGCGCACAACAATACCAATGAACATCGACCC A CATTTGAAGACGATCAAAAT B CACGGCCAACAACGTAAAGC C ACTAGGATCTCTAGTATTAG D ATGCAAGCCAAAAGTGTGAT E GATAGAATTGAGAATAACTC F CGCGCAGCAAATGCCCGATC G AACATCTCAGACTCGACAGA H AAGCAACTCCCCACAGAAAC ; End; BEGIN PAUP; [1] NJ; [2] LSCORE 1/ BASEFREQ=empirical TRATIO=estimate RATES=gamma SHAPE=estimate; [3] SET CRITERION=like; [4] LSET BASEFREQ=empirical TRATIO=previous RATES=gamma SHAPE=previous; [5] HSEARCH ADDSEQ=random NREPS=5 SWAP=TBR; END;