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https://github.com/arvestad/alv

A console-based alignment viewer
https://github.com/arvestad/alv

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A console-based alignment viewer

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# 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 v3.6 or later. Earlier versions may also work, but this has not been

tested.



## Latest feature additions



* If you have more than one alignment in your input file, then the first alignment is output unless you 

  use the --alignment-index (-ai) option to choose another.

* `alv` is now adapted for use in Python notebooks (tested on Jupyter) through two convenience functions

  'view' and 'glimpse'.  Both functions take a BioPython alignment object and outputs a view of the

  alignment.



  Writing

  ```

  from Bio import AlignIO

  msa = AlignIO.read('PF00005.fa', 'fasta')

  import alv

  alv.view(msa)

  ```

  in a Jupyter notebook cell and evaluating will yield a colored alignment in the `alv` style.



  For large alignments, the glimpse function is convenient since a subset of the alignment, selected

  as an easily detected conserved region, is shown.

  ```

  alv.glimpse(msa)

  ```

  Look for more usage information view `help(alv.view)` in a notebook cell. 



## 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.

* Focus on variable columns with the options `--only-variable` and

  `--only-variable-excluding-indels`, contributed by nikostr, that constrains

  coloring to columns with variation and variation not counting indels.

* 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.



## 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.



Choose to view a sub-alignment:

```

alv -sa 30 60 msa.fa

```

This selects and views columns 30 to 59 of msa.fa, keeping track of the "original" columns indexes in the output.



## For developers



* Run `pip install -e .` to get an "editable" install, while coding.

* Run `python -m build` to prepare a distributable file.



## 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)