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        "description": "# modelestimator --- Infer sequence evolution rate matrices from a MSA\n\n\n## Example usage\n\n``` shell\n    modelestimator -t 0.001 file1.fa file2.fa file3.fa\n```\nInfer a rate matrix (written to stdout) from three alignment files in Fasta format.\nThe output is PAML format by default, and therefore applicable in a number of\navailable phylogenetic softwares.\n\n``` shell\n    modelestimator -b 200 file.fa\n```\nTry the experimental bootstrapping feature (200 replicates) on a Fasta multialignment.\n\n## Syntax\n\n```\nmodelestimator <options> infiles\n```\n\n\n`<format>` should be either FASTA, STOCKHOLM or PHYLIP format.\n\nOutput is a rate matrix and residue distribution vector.\n\n### Options\n\n```\n  -h, --help            show this help message and exit\n  --version             show program's version number and exit\n  -a {iqtree,matlab,mrbayes,octave,paml,phyml}, --application {iqtree,matlab,mrbayes,octave,paml,phyml}\n                        Choose output format to suit the application you want\n                        to use for inference. The 'iqtree', 'paml' and 'phyml'\n                        options are identical. The 'matlab' and 'octave'\n                        optins are for import into MatLab-compatible programs\n                        and are presenting the actual Q matrix rather than the\n                        R matrix used by PAML/PhyML, etc. Default: paml\n  -f {fasta,clustal,nexus,phylip,stockholm}, --format {fasta,clustal,nexus,phylip,stockholm}\n                        Specify sequence format of input files. Default: fasta\n  -t T, --threshold T   Stop when consecutive iterations do not change by more\n                        than T. Default: 0.001\n  -b N, --bootstrap N   Estimate the rate matrix using bootstrapping by\n                        computing N resampled replicates of the input\n                        multialignment. For each replicate, a rate matrix is\n                        computed. The mean matrix the elementwise standard\n                        deviation is returned. Only one infile should be given\n                        in this mode.\n  -B N, --bootstrapped_quality N\n                        Estimate the quality of the rate matrix estimate using\n                        a bootstrap procedure. The multialignment is resampled\n                        N times and a Q matrix is computed for each replicate.\n                        Then the difference (matrix norm) between rate matrix\n                        estimated without resampling and each bootstrapped Q\n                        is computed and the mean difference is returned. Only\n                        one infile should be given in this mode. Returns\n                        bootstrap norm.\n```\n\n\n",
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