## 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. ## Availability`lapd` is distributed under the GNU General Public
License, and is available for immediate download. The software is a Perl
script that reads input, produces script files for, and pipes them to, Octave that does the actual computations. A fairly recent version of Octave is needed as the 'list' function must be supported.
Join the lapd mailing-list for notices about updates, communicating other users, etc! The list covers both lapd and modelestimator. Please acknowledge the use of LAPD in your research, preferably by citing this web site. ## Bootstrapping`lapd` is not a direct replacement
for `protdist` (from Phylip), and in particular it cannot
handle multiple datasets as is needed for Phylip-style
bootstrapping. For that purpose an accompanying program is available:
`bootstrap_lapd` . Like `lapd` , it is written in Perl. It repeatedly calls `lapd` on the datasets in its infile.
## UsageUsage: 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. |