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* New option: `-d` or `--dotted`: the first sequence in the output alignment is used as a template and for positions in subsequent sequences that are identical, a period ('.') is output instead of a symbol. * Adjustment: replacing blue with cyan in the DNA coloring scheme.
* 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.
* For some reason, setup.py was/is not putting proper Markdown to PyPi. Solved it halfway. Weird issue.
* Removed bug in alignmnent-type guessing: An MSA without any full codon would be guessed to be coding sequences.
* Ensured that alignment text color is black when starting. Helps for those other color preferences in the terminal.
* Adding self-promoting --cite and --methods options, noting that there is now a paper about `alv` in J Open Source Software.
* 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
* The option `-l` colors the alignment but does not break it into blocks. Suitable for piping to `less -RS`, as suggested by Mark McMullan <Mark.McMullanearlham.ac.uk>. * 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.
* 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 "-".
* 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.