alv - v1.8.0: support for sub-alignments

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

Scientific Software - Peer-reviewed - Python
Published by arvestad about 2 years ago

alv - v1.7.1

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

Scientific Software - Peer-reviewed - Python
Published by arvestad about 4 years ago

alv - 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.

Scientific Software - Peer-reviewed - Python
Published by arvestad about 4 years ago

alv - 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.

Scientific Software - Peer-reviewed - Python
Published by arvestad almost 5 years ago

alv - 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.

Scientific Software - Peer-reviewed - Python
Published by arvestad over 6 years ago

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

Scientific Software - Peer-reviewed - Python
Published by arvestad almost 7 years ago

alv - v1.3.0 — the official JOSS release

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

Scientific Software - Peer-reviewed - Python
Published by arvestad over 7 years ago

alv - 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.

Scientific Software - Peer-reviewed - Python
Published by arvestad over 7 years ago

alv - 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 Mark.McMullan@earlham.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.

Scientific Software - Peer-reviewed - Python
Published by arvestad almost 8 years ago

alv - 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".

Scientific Software - Peer-reviewed - Python
Published by arvestad almost 8 years ago

alv - First real release

This is the first real release, which has also been uploaded to pypi.org.

There is a discrepancy on the patch number in the version tag, but this is due to my negligence with committing setup.py and alv/version.py in due time. No need to be confused.

Scientific Software - Peer-reviewed - Python
Published by arvestad almost 8 years ago