MODELESTIMATOR: Estimating Amino Acid Replacement Rates
DescriptionThis program estimates amino acid replacement rates from an input of aligned sequences. The method is described in a forthcoming paper.
AvailabilityThe latest version of
The software is a Perl script that reads input, produces script files for, and pipes them to, Octave that does the actual computations.
Usage: modelestimator [<options>] <infile> [<outfile>] The infile should be in either FASTA, STOCKHOLM, or PHYLIP format. Output is a rate matrix and residue distribution vector, both in Octave/Matlab format. Options: -indels Remove gap columns. A gap is denoted by '-'. -threshold <f> Stop when consecutive iterations do not change by more than <f>. Default is 0.001. -paml Output model for use with PAML. -fasta Output substitution matrix (Pam250) for use with FastA. -v Verbose. Show progress info on STDERR. -octave <path> Point to the Octave binary to run. 'octave' by default. -d Debug option. Output Octave commands to STDOUT. -version Show version information. -u, -h This help text.