| 1 | TREE-PUZZLE 5.0 |
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| 2 | |
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| 3 | TREE-PUZZLE is a computer program to reconstruct phylogenetic trees |
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| 4 | from molecular sequence data by maximum likelihood. It implements a |
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| 5 | fast tree search algorithm, quartet puzzling, that allows analysis of |
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| 6 | large data sets and automatically assigns estimations of support to each |
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| 7 | internal branch. TREE-PUZZLE also computes pairwise maximum likelihood |
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| 8 | distances as well as branch lengths for user specified trees. Branch |
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| 9 | lengths can also be calculated under the clock-assumption. In addition, |
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| 10 | TREE-PUZZLE offers a novel method, likelihood mapping, to investigate |
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| 11 | the support of a hypothesized internal branch without computing an overall |
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| 12 | tree and to visualize the phylogenetic content of a sequence alignment. |
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| 13 | TREE-PUZZLE also conducts a number of statistical tests on the data set |
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| 14 | (chi-square test for homogeneity of base composition, likelihood ratio |
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| 15 | to test the clock hypothesis, Kishino-Hasegawa test). The models of |
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| 16 | substitution provided by TREE-PUZZLE are TN, HKY, F84, SH for |
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| 17 | nucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, |
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| 18 | and F81 for two-state data. Rate heterogeneity is modelled by a |
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| 19 | discrete Gamma distribution and by allowing invariable sites. |
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| 20 | The corresponding parameters can be inferred from the data set. |
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| 21 | |
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| 22 | INSTALLATION |
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| 23 | |
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| 24 | For compile an intall instructions see INSTALL and doc/manual.html |
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| 25 | |
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| 26 | In most cases on UNIX machines the following should work: |
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| 27 | |
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| 28 | sh ./configure |
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| 29 | make |
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| 30 | make intall |
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| 31 | |
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| 32 | |
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| 33 | |
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