School of
Computer Science
and Communication

MODELESTIMATOR: Estimating Amino Acid Replacement Rates


This program estimates amino acid replacement rates from an input of aligned sequences. The method is described in a forthcoming paper.


The latest version of modelestimator is found at the GitHub repository. The code is distributed under the GNU General Public License.

The software is a Perl script that reads input, produces script files for, and pipes them to, Octave that does the actual computations.

Please cite

if you use modelestimator!


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

   -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.

Published by: Lars Arvestad <>
Updated 2016-12-12