Metadata-Version: 2.1
Name: alv
Version: 1.5.1
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 your DNA or protein multiple-sequence alignments right at your command line. No need to launch a
        GUI!
        
        Note: `alv` requires Python v3.4 or later. Earlier versions may also work, but this has not been
        tested.
        
        ## Latest feature addition
        
        * The command `alv -g huge_msa.fa` displays cut-out of the MSA, guaranteed to fit
          one terminal page without scrolling or MSA line breaking, that is supposed to
          give you an idea of alignment quality and contents.
        * Write `alv -r 20 huge_msa.fa` to get a view of the MSA containing only 20 randomly
          selected sequences.
        
        ## Features
        
        * Command-line based, no GUI, so easy to script viewing of many (typically small) MSAs.
        * Reads alignments in FASTA, Clustal, PHYLIP, NEXUS, and Stockholm formats, from file or `stdin`.
        * 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.
        
        ## Install
        
        Recommended installation is:
        ```
        pip install --upgrade pip
        pip install alv
        ```
        
        If you have a half-modern BioPython installed, Python v3.4 _should_ work.
        BioPython is a dependency and will only get installed automatially with `pip install alv`
        if you are using Python v3.6 or later, because BioPython was apparently not on PyPi before that.
        
        
        ## Examples
        
        Quick viewing of a small alignment:
        ```
        alv msa.fa
        ```
        This autodetects sequence type (AA, DNA, RNA, coding DNA), colors the sequences, and formats the
        alignment for easy viewing in your terminal.
        When applying `alv` to an alignment of coding DNA, the coding property is autodetected and colors are therefore applied to codons instead
        of nucleotides.
        ![Seven coding DNA sequences](https://github.com/arvestad/alv/raw/master/doc/screenshot_2.png)
        
        
        
        View three sequences, accessions `a`, `b`, and `c`, from an alignment:
        ```
        alv -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.
        
        ## For developers
        
        Run `python setup.py develop test` for development install and to execute tests.
        
        ## Screenshots
        
        ### Full PFAM domain
        
        All of the sequences in PFAM's seed alignment for PF00005
        
        ![PF00005 seed MSA](https://github.com/arvestad/alv/raw/master/doc/screenshot_PF00005.png)
        
        ### Yeast sequences from PF00005
        
        Using the option `-sm YEAST`, we reduce the alignment to the ones with a matching accession.
        
        ![Small MSA from PF00005](https://github.com/arvestad/alv/raw/master/doc/PF00005_yeast.png)
        
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
