BioViz

Python 3.7 and Bokeh based visualization for Multiple Sequence Alignments

Usage

bioviz [-h] --file INPUT --type TYPE [--colors?] [--width PLOT_WIDTH] [--color COLOR_SCHEME] [--save] [--output OUTPUT] [--export EXPORT_FILE_TYPE]

Optional arguments:

• -h, --help show this help message and exit
• --file INPUT, -f INPUT Path to the file to used as input.
• --type TYPE, -t TYPE Define what type of figure should be created.
• --colors?, -c? List available color schemes.
• --width PLOT_WIDTH, -w PLOT_WIDTH For alignment and sequence logo figures defines the width in number of residues,for the dendogram it defines plot width in pixels.
• --color COLOR_SCHEME, -c COLOR_SCHEME Color scheme to use for the residues. Defaults to clustal
• --save, -s Only save the html file containing the fiugre, and do not automatically open it.
• --output OUTPUT, -o OUTPUT The name or full path including the file name to save the result.
• --export EXPORT_FILE_TYPE, -e EXPORT_FILE_TYPE Export the logo as PNG or SVG. SVG is not available for the sequence logo.

Diagram types:

• alignment Display the MSA file as plain sequence aligment.
• dendogram Create a dendogram from a dnd file
• seqlogo Create a sequence logo from the alignment.

Nucleotide color schemes:

• clustal
• macClade
• gcat
• purinePyrimidine
• translation
• annotation
• nucleotide

Protein color schemes:

• proteinClustal

• proteinZappo

• proteinTaylor

• proteinHydrophobicity

• proteinHelixPropensity

• proteinStrandPropensity

• proteinTurnPropensity

• proteinBuriedIndex