msa4u (version 0.4.0):
Simple visualisation tool for Multiple Sequence Alignments.
Home page and documentation:
https://github.com/art-egorov/msa4u
-------------------------------
COMMAND-LINE PARAMETERS
-------------------------------
[POST-INSTALL STEPS]
--data
    Creates the 'uorf4u_data' folder in the current working directory.
    The folder contains adjustable configuration files used by msa4u
    (e.g. config, palettes...)
--linux
    Replaces the mafft path in the pre-made config file from the MacOS'
    version [default] to the Linux'.
-------------------------------
[MANDATORY ARGUMENTS]
-fa <input.fa>
    Path to a fasta file with unaligned sequences.
    Alignment will be performed with mafft:
    [mafft --auto input.fa > input.aln.fa]
 OR
-aln <input.fa>
    Path to a fasta file with aligned sequences.
-------------------------------
[OPTIONAL ARGUMENTS]
-label <id|description|all>
    Label style based on input fasta file.
    id: sequence id from header (after > and before first space)
    description: after first space on header
    all: both (all header string)
-o-aln <filename>
    Alignment output filename.
    (used only if input is unaligned sequences)
    [default: auto; based on input file name]
-o <filename>
    Aligment visualisation filename.
    [default: auto; based on input file name]
-st <aa|nt|auto>
    Sequence type
    [default: auto; detected by used alphabet]
-c <standard|<file.cfg>
    Path to a configuration file or name of a premade config file
    [default: standard].
-------------------------------
[MISCELLANEOUS ARGUMENTS]
-h, --help
    Show this help message and exit.
-v, --version
    Show program version.
--debug
    Provide detailed stack trace for debugging purposes.
-q, --quiet
    Don't show progress messages.