phylogenetic alignment of homologous sequences alignment:multiple J. Hein Hein, J.: Unified approach to alignment and phylogenies. Meth. Enzymol. 183:626-645 (1990). Hein, J.: A new method that simultaneously aligns and reconstruct ancestral sequences for any number of homologous sequences, when the phylogeny is given. Mol. Biol. Evol. 6:649-668 (1989). Hein, J.: A tree reconstruction method that is economical in the number of pairwise comparisons used. Mol. Biol. Evol. 6:669-684 (1989). treealign treealign seqlab treealign perl "treealign" 0 param par.dat results *.ali *.tree fileseq Sequences File perl "$value\\n" 30 3 par.dat seqsfile perl 1 seqtype Sequence type perl "$value" 11 1 1: protein 0 0: DNA par.dat nuseq Number of sequences perl " $value" 12 par.dat gap_open Gap open penalty perl " $value" 13 Enter a non-negative value perl $value < 0 par.dat gap_ext Gap extension penalty perl " $value\\n" 14 par.dat other_options Other options ancesterout Present ancestral sequences perl ($value)? "1" : "0" 0 21 par.dat usertree User tree perl ($value)? " 1\\n" : " 0\\n" 0 22 par.dat usertreefile Your tree file perl "$value\\n" 60 perl $usertree par.dat filetree perl "$fileseq.tree\\n" 40 par.dat fileali perl "$fileseq.ali\\n" 50 par.dat