v1.8.0: support for sub-alignments

You can now run alv -sa 30 60 msa.fa to get columns 30 to 59 viewed.

v1.7.1

Nikos solved a bug: trailing N's disappeared when viewing DNA.

v1.7.0: notebook support and multi-MSA files

Two new features:

• Files containing multiple multialignments can now be handled. See the --alignment-index option.
• Two new functions that enable MSA viewing from within Jupyter notebooks.

v1.6.0: Focus on variable positions

The main addition in this release was contributed by @nikostr and lets you focus the colouring to variable positions only.

And for some reason, I never made the 1.5.0 release tagged here on github.

v1.4.0: Glimpse and randomly chosen sequences

• 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.

The let's-not-treat-all-borken-codons-as-coding-sequence release

v1.3.3

Updated to 1.3.4 for next patch

v1.3.0 — the official JOSS release

This is the release that corresponds to what is published in JOSS.

1.2.1 — the JOSS release

Some changes were made based on reviewer feedback when submitting to Journal of Open Source Software. Most notably, up-arrows for tick marks are not used when the console is not supporting UTF8.

1.2

• 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.

Release 1.1.0

Features added:

• Format detection
• Reading from stdin
• Shortening of accessions

This release is also pushed to pypi.org, see pypi.org/project/alv, install with "pip install alv".