https://github.com/lkremer/msa_trimmer

Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.
https://github.com/lkremer/msa_trimmer

aligned-regions alignment-trimming cds-alignment codeml codon-alignment molecular-evolution msa-trimmer multiple-sequence-alignment paml phylogenetics sequence-alignment trimmer trimming

Last synced: 3 months ago
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Straightforward & minimalistic removal of poorly aligned regions in sequence alignments.

• Host: GitHub
• URL: https://github.com/lkremer/msa_trimmer
• Owner: LKremer
• License: mit
• Created: 2017-06-02T11:32:35.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2019-03-18T16:10:36.000Z (over 6 years ago)
• Last Synced: 2025-05-09T02:43:40.073Z (5 months ago)
• Topics: aligned-regions, alignment-trimming, cds-alignment, codeml, codon-alignment, molecular-evolution, msa-trimmer, multiple-sequence-alignment, paml, phylogenetics, sequence-alignment, trimmer, trimming
• Language: Python
• Homepage:
• Size: 8.79 KB
• Stars: 17
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# MSA_trimmer: Straightforward & minimalistic removal of poorly aligned regions in **M**ultiple **S**equence **A**lignments

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 of

0.5 (``--trim_gappy 0.5``) would trim all columns where more than half of the sequences have a gap. You may also "hand-pick" columns

or 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 alignment

instead of trimming it. This will not remove any columns, instead the whole column will be replaced with

a 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 pair

of corresponding CDS and peptide alignments at the same time, to ensure the trimmed alignments will match. In that

case, 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 sequence

    alignments. Columns are removed if they exceed a user-specified "gappyness"

    treshold, and/or if they are specified by column index. Also works for codon

    alignments. The trimmed alignment is written to [your_alignment]_trimmed.fa

    optional 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: "-")