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Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
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LKremer/MSA_trimmer
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MSA_trimmer: Straightforward & minimalistic removal of poorly aligned regions inMultipleSequenceAlignments
This is a program to remove (trim) or mask columns of multiple sequence alignments in fasta format.Columns are removed if they exceed a user-specified "gappyness" treshold, i.e. a threshold of0.5 (--trim_gappy 0.5) would trim all columns where more than half of the sequences have a gap. You may also "hand-pick" columnsor whole regions of the alignment to be trimmed (--trim_positions).
If you want to preserve the original coordinates of the alignment, you may also chose to "mask" your alignmentinstead of trimming it. This will not remove any columns, instead the whole column will be replaced witha character of your choice (the gap character "-" by default).
Trimming works for both nucleotide/codon/CDS (-c) and peptide (-p) alignments. You may even trim a pairof corresponding CDS and peptide alignments at the same time, to ensure the trimmed alignments will match. In thatcase, only whole codons (chunks of three bases each) will be removed in order not to introduce a frame shift.This is useful for applications that need a codon alignment such as CODEML.
usage: alignment_trimmer.py [-h] [-p PEP_ALIGNMENT_FASTA] [-c CDS_ALIGNMENT_FASTA] [--trim_gappy TRIM_GAPPY] [--trim_positions TRIM_POSITIONS [TRIM_POSITIONS ...]] [--mask [MASK]]A program to remove (trim) or mask columns of fasta multiple sequencealignments. Columns are removed if they exceed a user-specified "gappyness"treshold, and/or if they are specified by column index. Also works for codonalignments. The trimmed alignment is written to [your_alignment]_trimmed.faoptional arguments:-h, --help show this help message and exit-p PEP_ALIGNMENT_FASTA, --pep_alignment_fasta PEP_ALIGNMENT_FASTA-c CDS_ALIGNMENT_FASTA, --cds_alignment_fasta CDS_ALIGNMENT_FASTA--trim_gappy TRIM_GAPPY the maximum allowed gap proportion for an MSA column, all columns with a higher proportion of gaps will be trimmed (default: off)--trim_positions TRIM_POSITIONS [TRIM_POSITIONS ...] specify columns to be trimmed from the alignment, e.g. "1-10 42" to trim the first ten columns and the 42th column--mask [MASK] mask the alignment instead of trimming. if a character is specified after --mask, that character will be used for masking (default char: "-")