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Program for estimating amino acid replacement rates

Project description

# modelestimator --- Infer sequence evolution rate matrices from a MSA

## Example usage

``` shell
modelestimator -t 0.001 file1.fa file2.fa file3.fa
Infer a rate matrix (written to stdout) from three alignment files in Fasta format.

``` shell
modelestimator -b 200 file.fa
Try the experimental bootstrapping feature (200 replicates) on a Fasta multialignment.

## Syntax

modelestimator <options> infiles

`<format>` should be either FASTA, STOCKHOLM or PHYLIP format.

Output is a rate matrix and residue distribution vector.

### Options

-h, --help show this help message and exit
--version show program's version number and exit
-a {iqtree,matlab,mrbayes,octave,paml,phyml}, --application {iqtree,matlab,mrbayes,octave,paml,phyml}
Choose output format to suit the application you want
to use for inference. The 'iqtree', 'paml' and 'phyml'
options are identical. The 'matlab' and 'octave'
optins are for import into MatLab-compatible programs
and are presenting the actual Q matrix rather than the
R matrix used by PAML/PhyML, etc. Default: paml
-f {fasta,clustal,nexus,phylip,stockholm}, --format {fasta,clustal,nexus,phylip,stockholm}
Specify sequence format of input files. Default: fasta
-t T, --threshold T Stop when consecutive iterations do not change by more
than T. Default: 0.001
-b N, --bootstrap N Estimate the rate matrix using bootstrapping by
computing N resampled replicates of the input
multialignment. For each replicate, a rate matrix is
computed. The mean matrix the elementwise standard
deviation is returned. Only one infile should be given
in this mode.
-B N, --bootstrapped_quality N
Estimate the quality of the rate matrix estimate using
a bootstrap procedure. The multialignment is resampled
N times and a Q matrix is computed for each replicate.
Then the difference (matrix norm) between rate matrix
estimated without resampling and each bootstrapped Q
is computed and the mean difference is returned. Only
one infile should be given in this mode. Returns
bootstrap norm.

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