2.1 Reconstructing Evolution With Parsimony And Simulated Annealing D. Barker Barker, D. 2004. LVB: Parsimony and simulated annealing in the search for phylogenetic trees. Bioinformatics, 20, 274-275. phylogeny lvb lvb perl "lvb < params" 0 infile Alignement File perl "ln -sf $infile infile; " -10 11 12 You had better provide a Phylip 3.6, MSF or FASTA formatted alignment. Clustalw format will ***not*** work for this service. You may use the readseq form on the same server to convert your clustalw alignment to a Phylip INTERLEAVED format (#12). format Format is INTERLEAVED or SEQUENTIAL 1 perl "$value\\n" I I INTERLEAVED S SEQUENTIAL params gaps_treatment Treatment of gaps represented by '-' 2 perl "$value\\n" U U UNKNOWN F FIFTH STATE A gap represented by the letter 'O' in the data matrix is always treated as a character state in its own right (fifth state). lvb can treat gaps represented by '-' in either of the following ways: Fifth state '-' is treated as equivalent to 'O'. Unknown '-' is treated as equivalent to '?', i.e., as an ambiguous site that may contain 'A' or 'C' or 'G' or 'T' or 'O'. 'Fifth state' may give excessive weight to multi-site gaps, since each affected base will be counted as one event. params seed Seed for the random number generator (seed) 3 perl (defined $value)? "$value\\n" : "\\n" When prompted for the random number seed, enter an integer in the range 0 to 900000000 inclusive. The default value is taken from the system clock and hence will vary from one analysis to the next, changing every second. The default is usually appropriate. params duration Duration of the analysis FAST or SLOW 4 perl "$value\\n" F F FAST S SLOW Please choose the duration of the analysis. If the data matrix contains a large number of sequences, a SLOW analysis might find a shorter tree. params bootstrap How many bootstrap replicates required (bootstrap) 5 perl "$value\\n" 0 this server allows no more than 1000 replicates perl $bootstrap > 1000 Number of bootstrap replicates required as an integer in the range 1 to 1000 inclusive, or 0 for no bootstrapping (this server allows no more than 1000 replicates) params params params res outtree phylip_tree perl 1 other_results stat* sum log data ini*