Metadata-Version: 2.1
Name: alv
Version: 1.0.1
Summary: A console-based sequence alignment viewer
Home-page: https://github.com/arvestad/alv
Author: Lars Arvestad
Author-email: arve@math.su.se
License: UNKNOWN
Description: # alv: a command-line alignment viewer
        
        View you DNA or protein multiple-sequence alignments right at your command line. No need to launch a
        GUI!
        
        Features:
        
        * Command-line based, no GUI, so easy to script viewing of many (typically small) MSAs.
        * Reads alignments in FASTA, Clustal, PHYLIP, and Stockholm formats. 
        * Output is formatted to suit your terminal. You can also set the alignment width with option `-w`.
        * Can color alignments of coding DNA by codon's translations to amino acids.
        * Guesses sequence type (DNA/RNA/AA/coding) by default. You can override with option `-t`.
        * Order sequence explicitly, alphabetically, or by sequence similarity.
        * Restrict coloring to where you don't have indels or where there is a lot of conservation.
        
        ## Examples
        
        Quick viewing of a small alignment:
        ```
        alf msa.fa
        ```
        This autodetects sequence type (AA, DNA, RNA, coding DNA), colors the sequences, and formats the
        alignment for easy viewing in your terminal.
        
        View three sequences, accessions `a`, `b`, and `c`, from an alignment:
        ```
        alf -so a,b,c msa.fa
        ```
        
        Feed alignment to `less`, for paging support.
        ```
        alv -k msa.fa | less -R
        ```
        The `-k` option ensures that `alv` keeps coloring the alignment (by default, piping
        and redirection removes colors), and the `-R` option instructs `less` to interpret color codes.
        
        ## Install
        
        Recommended installation is with `pip install alv`.
        
        ## For developers
        
        Run `python setup.py develop test` for development install and to execute tests.
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
Description-Content-Type: text/markdown
