The programs in lintre.tar are for (1) testing the molecular clock on a given topology of a phylogenetic tree and (2) making linearized trees (reestimating branch lengths under the assumption of constant rate of evolutions. The data that can be used are nucleotide or amino acid sequences. Note that the programs run on Sun workstations at least for now. For details of the methods, please look at "Phylogenetic tests of the molecular clock and linearized trees" (Molecular Biology and Evolution 12: 823-833, 1995). (1) Ftp lintre.tar and lintre.readme onto your system in the binary mode. (2) Type "uncompress lintre.tar.Z". (3) Type "tar xvf lintre.tar". (4) Read the read.me file first. If you have problems or comments, please send email to: takezaki@imeg.bio.psu.edu October 4, 1995 Naoko Takezaki 322 Mueller Penn State University University Park, PA 16802 USA FAX 814(863)7336 +--------------------------------------------------------------------+ | Phylogenetic tests of the molecular clock and linearized tree | +--------------------------------------------------------------------+ These programs run on Sun workstations. This directory have five programs: njboot -- construct a neighbor-joining (NJ) tree postree -- create a postscript file of trees tpcv -- conduct the two-cluster test branch -- conduct the branch length test branbst -- conduct the branch length test by bootstrap and example files: crab.dat -- 13 mtDNA sequences of crab species crab.nj -- an NJ treefile of the crab sequences crab.tc -- output of tpcv (result of the two-cluster test) crab.dat.cn -- output of tpcv (linearized tree) crab.br -- output of branch (result of the branch length test) crab.br.ps -- postscript file for crab.br (output of postree) Make sure that you use the binary mode when you ftp the files. After copying the files on your system, type chmod 711 njboot postree tpcv branch branbst There are two tests of rate constancy: (1) two-cluster test and (2) branch length test. The two-cluster test is essentially the relative rate test for many sequences. The branch length test is the test of rate difference for each sequence under the tree root from the average rate of all sequences. The two tests assume that the tree topology is given and that the ougroup is known so that the root of the tree is also known. Thus, to carry out these tests, first construct a neighbor-joinig (NJ) tree. (1) sequence inputfile for njboot, tpcv, branch, and branbst The file format is just like the PHYLIP package format without the number of sequences and the number of sites, but sequence names and actual data should be separated by at least one space. All sequences should have the same number of sites.