LAPD LAPD program estimates pairwise distances for a set of protein sequences.
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DISTANCES protein sequences pairwise distances estimates distances LAPD pairwise

LAPD Description

LAPD program estimates pairwise distances for a set of protein sequences. LAPD 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.Usage:Usage: lapd < 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 "Speed". High speed results in low precision. Default is 5. Valid range is . -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.

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