Metadata-Version: 2.1
Name: modelmatcher
Version: 1.1.2
Summary: Rapid identification of sequence evolution models
Home-page: https://github.com/arvestad/modelmatcher
Author: Lars Arvestad
Author-email: arve@math.su.se
License: UNKNOWN
Description: # modelmatcher: Rapid identification of evolutionary models
        
        This tool reads multiple sequence alignments and determines a suitable sequence
        evolution model for your phylogenetic analysis.
        
        ## Usage
        
        Example usage:
        
        ``` shell
        $ modelmatcher inputfile.fasta
        ```
        
        The input file is a multiple sequence alignmnent in one of these common formats:
        
        * FASTA
        * Clustal
        * NEXUS
        * PHYLIP
        * STOCKHOLM
        
        The output is a list of models, in order of fit to data, and their modelmatcher score.
        The base model (such as JTT, WAG, LG, etc) is predicted, as well as whether one should
        adapt to the alignments amino acid composition (i.e., JTT+F, WAG+F, etc).
        
        ### Options
        
        Optional options:
        ```
          -h, --help            show this help message and exit
          -f {guess,fasta,clustal,nexus,phylip,stockholm}, --format {guess,fasta,clustal,nexus,phylip,stockholm}
                                Specify what sequence type to assume. Be specific if
                                the file is not recognized automatically. When reading
                                from stdin, the format is always guessed to be FASTA.
                                Default: guess
          -m filename, --model filename
                                Add the model given in the file to the comparisons.
          -nf, --no-F-testing   Do not try +F models, i.e., do not test with amino
                                acid frequencies estimated from the MSA.
          -of {tabular,json,iqtree,raxml,phyml,mrbayes}, --output_format {tabular,json,iqtree,raxml,phyml,mrbayes}
                                Choose output format. Tabular format is default. JSON
                                is for convenient later parsing, with some additional
                                meta-data added. For one-line output convenient for
                                immediate use by inference tools, consider raxml and
                                similar choices. Note that the PhyML and MrBayes
                                options are restricted to their implemented models.
                                Although PhyML supports the +F models (using the "-f
                                e" option), this is not reflected in the output from
                                "modelmatcher -of phyml ..." at this time.
          --verbose             Output progress information
        ```
        
        
        
        ### Input formats
        
        Input format is detected automatically from the following list, but can also be
        requested specifically.
        
        * FASTA
        * Phylip
        * Nexus
        * Clustal
        * Stockholm
        
        ### Output
        
        Output is given as a simple text table, or in JSON format for easy parsing by
        other scripts, ranking possible models in preference order. For example, the command above may yield a table looking like:
        
        ```
        WAG             7.972
        VT              8.238
        BLOSUM62        8.478
        JTT             8.864
        JTT-DCMUT       8.917
        LG              9.984
        DCMUT          10.467
        Dayhoff        10.495
        FLU            11.211
        HIVb           12.853
        RtREV          14.048
        cpREV          14.186
        HIVw           17.338
        MtZoa          18.476
        MtMAM          21.453
        mtArt          21.741
        MtREV          22.059
        ```
        Each model is given with its modelmatcher score.
        
        Alternatively, the same analysis can look like:
        
        ``` shell
        $ modelmatcher  --json  inputfile.fasta
        {"n_observations": 863692, "infile": "inputfile.fasta", "n_seqs": 66, "model_ranking": [["WAG", 7.972410383355675], ["VT", 8.238362164888876], ["BLOSUM62", 8.478000205922985], ["JTT", 8.863578165338444], ["JTT-DCMUT", 8.917496451351846], ["LG", 9.983874357603963], ["DCMUT", 10.466872509785343], ["Dayhoff", 10.49522598111376], ["FLU", 11.21137482805874], ["HIVb", 12.852877789672046], ["RtREV", 14.047539707772572], ["cpREV", 14.18648653904322], ["HIVw", 17.338193829402], ["MtZoa", 18.475515151949153], ["MtMAM", 21.452528293860837], ["mtArt", 21.740741039472418], ["MtREV", 22.058622800684176]]}
        ```
        
        
        ## Install
        
        Recommended installation is:
        ```
        pip install --upgrade pip
        pip install modelmatcher
        ```
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.2
Description-Content-Type: text/markdown
