Metadata-Version: 2.1
Name: modelmatcher
Version: 1.0
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
        ```
        
        ### Options
        
        
        ### 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 alv
        ```
        
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
