TREE-PUZZLE 5.2TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements afast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to eachinternal branch. TREE-PUZZLE also computes pairwise maximum likelihood distances as well as branch lengths for user specified trees. Branchlengths can also be calculated under the clock-assumption. In addition, TREE-PUZZLE offers a novel method, likelihood mapping, to investigatethe support of a hypothesized internal branch without computing an overall tree and to visualize the phylogenetic content of a sequence alignment.TREE-PUZZLE also conducts a number of statistical tests on the data set (chi-square test for homogeneity of base composition, likelihood ratioto test the clock hypothesis, Kishino-Hasegawa test). The models of substitution provided by TREE-PUZZLE are TN, HKY, F84, SH fornucleotides, Dayhoff, JTT, mtREV24, BLOSUM 62, VT, WAG for amino acids, and F81 for two-state data. Rate heterogeneity is modelled by adiscrete Gamma distribution and by allowing invariable sites. The corresponding parameters can be inferred from the data set. INSTALLATIONFor compile an intall instructions see INSTALL and doc/manual.htmlIn most cases on UNIX machines the following should work(if the prefix is left out configure the executable are installedin /urs/local): sh ./configure --prefix=/usr/local make make install