## 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.## Availability`modelestimator` is distributed under the GNU General Public
License, and is available for
immediate download. This is version 1.1, which improves on
version 1.0 by fixing a bug regarding scaling of the rate matrix and
work on recent versions of Octave (cell arrays are used
instead of deprecated lists.)
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 cite - Lars Arvestad,
, 2006, J Mol Evol, 62(6):663–673.**Efficient methods for estimating amino acid replacement rates**
`modelestimator` !
## UsageUsage: 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. |