Metadata-Version: 2.1
Name: phylopypruner
Version: 0.1
Summary: tree-based orthology inference
Home-page: https://gitlab.com/fethalen/phylopypruner
Author: Felix Thalen
Author-email: fe1430th-s@student.lu.se
License: MIT
Description: PhyloPyPruner
        -------------
        
        PhyloPyPruner is a phylogenetic tree-based orthology inference program for
        refining orthology inference made by graph-based (or phenetic) approaches.
        
        PhyloPyPruner is under active development. I would appreciate it if you try
        this software on your own data and [leave
        feedback](mailto:felix.thalen.1430@student.lu.se).
        
        To get a list of options, either run the software without any parameters or by
        using the `-h` or `--help` flag. For more details, please see [the
        Wiki](https://gitlab.com/fethalen/phylopypruner/wikis).
        
        ### Features
        
        * Remove short sequences
        * Remove sequences with long branches
        * Collapse weakly supported nodes into polytomies
        * Five different paralogy pruning algorithms
        * Measure and remove OTUs with frequent paralogs
        * Identify problematic OTUs using taxon jackknifing
        * Exclude certain OTUs
        * Specify taxonomical groups and see how often they form a phylogenetic group
        * Mask monophylies by choosing the longest sequence or using pairwise distance
        
        ### Input data
        
        Either provide a single multiple sequence alignment (MSA) and a Newick tree by
        using the `--msa` and `--tree` flags:
        
        ```
        ./phylopypruner --msa 16s.fas --tree 16s.tre
        ```
        
        or, provide a `path` to an input directory, containing multiple trees and
        alignments, by typing `--dir path`.
        
        FASTA descriptions and Newick names must match and has to be in one of the
        following formats: `OTU|ID` or `OTU@ID`, where `OTU` is the operational
        taxonomical unit (usually the species) and `ID` is a unique annotation or
        sequence identifier. For example: `>Meiomenia_swedmarki|Contig00001_Hsp90`.
        
        Sequence descriptions and tree names are not allowed to deviate from each
        other. Sequence data needs to be [valid IUPAC nucleotide or amino acid
        sequences](https://www.bioinformatics.org/sms/iupac.html).
        
        For inputting multiple files, you provide a path to the directory in which
        these files reside.
        
        ```
        ./phylopypruner --dir <path>
        ```
        
        The program will automatically look for trees and alignments with the same name
        and run for each of these pair.
        
        ### Output files
        
        The following files are generated after running this program:
        
        * `<timestamp>_<orthologs>/...` – output alignments
        * `<timestamp>_ppp_summary.log` – summary statistics for all alignments
        * `<timestamp>_ppp_run.log` – detailed report of each performed action
        * `<timestamp>_ppp_ortho_stats.csv` – statistics for output alignments
        * `<timestamp>_ppp_paralog_freq.csv` – paralogy frequency data
        * `<timestamp>_ppp_paralog_freq.png` – paralogy frequency plot\*
        
        \* – only produced if [Matplotlib](https://matplotlib.org/) is installed
        
        © [Kocot Lab](https://www.kocotlab.com/) 2018
        
Keywords: orthology inference,orthologs,tree-based,phylogenetics,phylogenomics,orthology
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
