LAPD: Estimating Protein Distances
DescriptionThis program estimates pairwise distances for a set of protein sequences. The output can be used in conjunction with other phylogeny programs, such as Phylip.
A special feature is that the specialized rate matrices, estimated by modelestimator, can be used as input to the program.
The method is described in a forthcoming paper.
Please acknowledge the use of LAPD in your research, preferably by citing this web site.
Usage: lapd [<options>] <infile> The infile should be in either FASTA, STOCKHOLM, or PHYLIP format. Output is a matrix of expected distances and, if possible, estimates of standard deviation. Options: -indels Remove gap columns. A gap is denoted by '-'. -ml Compute a Maximum Likelihood estimate instead. This option implies -sd. -sd Do not output a matrix with standard deviations after the distance matrix. -id Output percent identity. -jc Use a simplistic Jukes-Cantor model. -jck Use -jc, but use Kimura's correction. -jcss Like -jck, but using Storm-Sonhammer's correction. -wag Default. Use the WAG matrix (see Wheelan and Goldman, 2001). -jtt Use the JTT matrix (see Jones, Taylor, Thornton, 1992). -day Use the Dayhoff matrix (Dayhoff et al, 1978). -arve Use the Arvestad matrix. -mv Use the Muller-Vingron matrix (2000). -f <file> Read matrix and equilibrium distribution from file. -pfam Use a normal distribution as distance prior, estimated from Pfam 7.2. -s <int> "Speed". High speed results in low precision. Default is 5. Valid range is [1, 10]. -v Verbose. Show progress info on STDERR. -octave <path> Point to the Octave binary to run. 'octave -q' by default. -d Debug option. Output Octave commands to STDOUT. -u, -h This help text.