cialign 0.1.0

Toolkit for cleaning and interpreting multiple sequence alignments

CIAlign

CIAlign is a command line tool which performs various functions to parse and analyse a multiple sequence alignment (MSA).

The tool is designed to be highly customisable, allowing users to specify exactly which functions to run and which settings to use. It is also transparent, generating a clear log file and diagram showing exactly how the alignment has changed.

This allows the user to:

• Remove sources of noise from their MSA

  • Crop of poorly aligned sequence ends
  • Remove of insertions which are not present in the majority of sequences
  • Remove of sequences below a threshold number of bases or amino acids
  • Remove columns containing only gaps
  • Remove sequences above a threshold level percentage of divergence from the majority

• Generate consensus sequences

• Visualise alignments

  • Generate image files showing the alignment before and after parsing and showing which columns and rows have been removed
  • Draw sequence logos
  • Visualise coverage at each postiion in the alignment

• Analyse alignment statistics

  • Generate a similarity matrix showing the percentage identity between each sequence pair

Requirements

• python >= 3.6
• matplotlib >= 2.1.1
• numpy >= 1.16.3
• scipy >= 1.3.0

Installation

The current release of CIAlign can be downloaded directly using this link

Add the CIAlign directory to your PATH environment variable as described here

Usage

Basic Usage

CIAlign --infile INFILE --outfile_stem STEM --inifile my_config.ini

Parameters

Parameters can be specified in the command line or in a config file using the naming system below.

A template config file is provided in CIAlign/templates/ini_template.txt - edit this file and provide the path to the --inifile argument. If this argument is not provided command line arguments and defaults will be used.

Parameters passed in the command line will take precedence over config file parameters, which take precedence over defaults.

Command help can be accessed by typing CIAlign --help

Parameter	Description	Default
--infile	Path to input alignment FASTA file	None
--inifile	Path to ini file	None
--outfile_stem	Prefix for output files, including the path to the output directory	CIAlign
--silent	Do not print progress to the screen	False

Functions

Specify which functions to run by adding the following optional arguments to the command

Parsing an MSA

Each of these steps will be performed sequentially in the order specified in the table below.

The parsed alignment after all steps have been performed will be saved as OUTFILE_STEM_parsed.fasta

Parameter	Description	Default Value
--crop_ends	Crop the ends of sequences if they are poorly aligned	False
--crop_ends_mingap	minimum gap size to consider when classifying a sequence as poorly aligned	10
--remove_badlyaligned	Remove sequences with <= N proportion of positions at which the most common base / amino acid in the alignment is present	False
--remove_badlyaligned_minperc	Minimum proportion of positions which should be identical to the most common base / amino acid in order to be preserved	0.9
--remove_insertions	Remove insertions found in <= 50% of sequences from the alignment	False
--insertion_min_size	Only remove insertions >= this number of residues	3
--insertion_max_size	Only remove insertions <= this number of residues	300
--insertion_min_flank	Minimum number of bases on either side of an insertion to classify it as an insertion	5
--remove_short	Remove sequences <= N bases / amino acids from the alignment	False
--remove_minlength	Minimum number of non-gap residues in a sequence to be preserved	50
--remove_gaponly	Remove gap only columns from the alignment	True

Generating a Consensus Sequence

This step generates a consensus sequence based on the parsed alignment. If no parsing functions are performed, the consensus will be based on the input alignment.

Output files:

• OUTFILE_STEM_consensus.fasta - the consensus sequence only
• OUTFILE_STEM_with_consensus.fasta - the parsed alignment plus the consensus

Parameter	Description	Default
--make_consensus	Make a consensus sequence based on the parsed alignment	False
--consensus_type	Type of consensus sequence to make - can be majority, to use the most common character at each position in the consensus, even if this is a gap, or majority_nongap, to use the most common non-gap character at each position	majority
--consensus_keepgaps	If there are gaps in the consensus (if majority_nongap is used as consensus_type), should these be included in the consensus (True) or should this position in the consensus be deleted (False)	False
--consensus_name	Name to use for the consensus sequence in the output fasta file	consensus

Visualising Alignments

Each of these functions produces some kind of visualisation of your alignment.

Mini Alignments

These functions produce "mini alignments" - images showing a small representation of your whole alignment, so that gaps and poorly aligned regions are clearly visible.

Output files:

• OUTFILE_STEM_input.png (or svg, tiff, jpg) - the input alignment
• OUTFILE_STEM_output.png (or svg, tiff, jpg) - the parsed output alignment
• OUTFILE_STEM_markup.png (or svg, tiff, jpg) - the input alignment with deleted rows and columns marked

Parameter	Description	Default
--plot_input	Draws a mini alignment for the input FASTA file	False
--plot_output	Draws a mini alignment for the output FASTA file	False
--plot_markup	Draws the input alignment but with the columns and rows which have been removed by each function marked	False
--plot_dpi	DPI for mini alignments	300
--plot_format	Image format for mini alignments - can be png, svg, tiff or jpg	png
--plot_width	Mini alignment width in inches	5
--plot_height	Mini alignment height in inches	3

Sequence logos

These functions draw sequence logos representing your output (parsed) alignment. If no parsing functions are specified, the logo will be based on your input alignment.

Output_files:

• OUTFILE_STEM_logo_bar.png (or svg, tiff, jpg) - the alignment represented as a bar chart
• OUTFILE_STEM_logo_text.png (or svg, tiff, jpg) - the alignment represented as a standard sequence logo using text

Parameter	Description	Default
--make_sequence_logo	Draw a sequence logo	False
--sequence_logo_type	Can be bar, to draw the logo as a bar chart, text, to draw a standard sequence logo using text, or both, to draw both	bar
--sequence_logo_dpi	DPI for sequence logo	300
--sequence_logo_font	font (see NB below) for bases / amino acids in a text based sequence logo	monospace
--sequence_logo_nt_per_row	number of bases / amino acids to show per row in the sequence logo, where the logo is too large to show on a single line	50
--sequence_logo_filetype	Image file type to use for the sequence logo - can be png, svg, tiff or jpg	png

NB: to see available fonts on your system, run CIAlign --list_fonts_only and view CIAlign_fonts.png

Coverage Plots

This function plots the number of non-gap residues at each postion in the alignment.

Output file:

• OUTFILE_STEM_input_coverage.png (or svg, tiff, jpg) - image showing the input alignment coverage
• OUTFILE_STEM_output_coverage.png (or svg, tiff, jpg) - image showing the parsed alignment coverage

Parameter	Description	Default
--plot_coverage_input	Plot the coverage of the multiple sequence alignment	False
--plot_coverage_output	Plot the coverage of the multiple sequence alignment	False
--plot_coverage_dpi	DPI for coverage plot	300
--plot_coverage_height	Height for coverage plot (inches)	3
--plot_coverage_width	Width for coverage plot (inches)	5
--plot_coverage_colour	Colour for coverage plot (hex code or name)	#007bf5
--plot_coverage_filetype	File type for coverage plot (can be png, svg, tiff, jpg)	png

Analysing Alignment Statistics

These functions provide additional analyses you may wish to perform on your alignment.

Similarity Matrices

Generates a matrix showing the proportion of identical bases / amino acids between each pair of sequences in the MSA.

Output file:

• OUTFILE_STEM_input_similarity.tsv - similarity matrix for the input file
• OUTFILE_STEM_output_similarity.tsv - similarity matrix for the ouput file

Parameter	Description	Default
--make_similarity_matrix_input	make a similarity matrix for the input alignment	False
--make_similarity_matrix_output	make a similarity matrix for the output alignment	False
--make_simmatrix_keepgaps	Include positions with gaps in either or both sequences in the similarity calculation	False
--make_simmatrix_dp	Number of decimal places to display in the similarity matrix output file	4
--make_simmatrix_minoverlap	Minimum overlap between two sequences to have non-zero similarity in the similarity matrix	1