Changes since last version

v1.4.0

New option: -r k or --random-accessions k for only showing a sample of k sequences.
New option: -g or --glimpse: display an informative cut-out of the input MSA, if it does not fit without scrolling or line-breaking.

v1.3.4

For some reason, setup.py was/is not putting proper Markdown to PyPi. Solved it halfway. Weird issue.

v1.3.3

Removed bug in alignmnent-type guessing: An MSA without any full codon would be guessed to be coding sequences.

v1.3.2

Ensured that alignment text color is black when starting. Helps for those other color preferences in the terminal.

v1.3.1

Adding self-promoting --cite and --methods options, noting that there is now a paper about alv in J Open Source Software.

v1.3

Tick marks come out as ^ on non-UTF systems, instead of an up-arrow on UTF systems (decided by looking at $LANG).
Support for Nexus files added (thanks @SimonGreenhill)
Added CONTRIBUTING.md, a text on how to help develop alv.
Better README

v1.2.0

The option -l colors the alignment but does not break it into blocks. Suitable for piping to less -RS, as suggested by Mark McMullan [email protected].
More indices indicated below alignments, and with an up-arrow as a tick mark.
Added option -sm to allow restricting output to sequences with accessions containing a given string.

v1.1.0

Implemented format guessing. By default, alv tries to identify the alignment format. You can still override if there are parsing problems.
You can specify what part of accessions to view with -as. This way you can avoid common prefixes and easily shorten long accessions.
View only the first and last N characters of accessions with option -aa.
Read from stdin with the magic file name "-".

Introduced in version 1.0.5

Explicitly start with "/usr/bin/env python3" instead of "/usr/bin/env python". Hoping that will help users that have not yet migrated to v3.
Added v3 requirement in setup.py as well, using advice from Tobias Jakobi. Solves issue #1 on github.com.