{"id":20844852,"url":"https://github.com/lkremer/msa_trimmer","last_synced_at":"2025-07-06T10:03:38.960Z","repository":{"id":83467474,"uuid":"93159524","full_name":"LKremer/MSA_trimmer","owner":"LKremer","description":"Straightforward \u0026 minimalistic removal of poorly aligned regions in sequence alignments.","archived":false,"fork":false,"pushed_at":"2019-03-18T16:10:36.000Z","size":9,"stargazers_count":17,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-05-09T02:43:40.073Z","etag":null,"topics":["aligned-regions","alignment-trimming","cds-alignment","codeml","codon-alignment","molecular-evolution","msa-trimmer","multiple-sequence-alignment","paml","phylogenetics","sequence-alignment","trimmer","trimming"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/LKremer.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-06-02T11:32:35.000Z","updated_at":"2024-09-26T14:57:57.000Z","dependencies_parsed_at":null,"dependency_job_id":"90667b52-b2ae-4ed5-a7f3-2842d2baedc0","html_url":"https://github.com/LKremer/MSA_trimmer","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/LKremer/MSA_trimmer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LKremer%2FMSA_trimmer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LKremer%2FMSA_trimmer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LKremer%2FMSA_trimmer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LKremer%2FMSA_trimmer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LKremer","download_url":"https://codeload.github.com/LKremer/MSA_trimmer/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LKremer%2FMSA_trimmer/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263882261,"owners_count":23524459,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["aligned-regions","alignment-trimming","cds-alignment","codeml","codon-alignment","molecular-evolution","msa-trimmer","multiple-sequence-alignment","paml","phylogenetics","sequence-alignment","trimmer","trimming"],"created_at":"2024-11-18T02:11:15.117Z","updated_at":"2025-07-06T10:03:38.941Z","avatar_url":"https://github.com/LKremer.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MSA_trimmer: Straightforward \u0026amp; minimalistic removal of poorly aligned regions in **M**ultiple **S**equence **A**lignments\nThis is a program to remove (trim) or mask columns of multiple sequence alignments in fasta format.\nColumns are removed if they exceed a user-specified \"gappyness\" treshold, i.e. a threshold of\n0.5 (``--trim_gappy 0.5``) would trim all columns where more than half of the sequences have a gap. You may also \"hand-pick\" columns\nor whole regions of the alignment to be trimmed (``--trim_positions``).\n\nIf you want to preserve the original coordinates of the alignment, you may also chose to \"mask\" your alignment\ninstead of trimming it. This will not remove any columns, instead the whole column will be replaced with\na character of your choice (the gap character \"-\" by default).\n\nTrimming works for both nucleotide/codon/CDS (``-c``) and peptide (``-p``) alignments. You may even trim a pair\nof corresponding CDS and peptide alignments at the same time, to ensure the trimmed alignments will match. In that\ncase, only whole codons (chunks of three bases each) will be removed in order not to introduce a frame shift.\nThis is useful for applications that need a codon alignment such as CODEML.\n\n    usage: alignment_trimmer.py [-h] [-p PEP_ALIGNMENT_FASTA]\n                                [-c CDS_ALIGNMENT_FASTA] [--trim_gappy TRIM_GAPPY]\n                                [--trim_positions TRIM_POSITIONS [TRIM_POSITIONS ...]]\n                                [--mask [MASK]]\n\n    A program to remove (trim) or mask columns of fasta multiple sequence\n    alignments. Columns are removed if they exceed a user-specified \"gappyness\"\n    treshold, and/or if they are specified by column index. Also works for codon\n    alignments. The trimmed alignment is written to [your_alignment]_trimmed.fa\n\n    optional arguments:\n    -h, --help            show this help message and exit\n    -p PEP_ALIGNMENT_FASTA, --pep_alignment_fasta PEP_ALIGNMENT_FASTA\n    -c CDS_ALIGNMENT_FASTA, --cds_alignment_fasta CDS_ALIGNMENT_FASTA\n    --trim_gappy TRIM_GAPPY\n                            the maximum allowed gap proportion for an MSA column,\n                            all columns with a higher proportion of gaps will be\n                            trimmed (default: off)\n    --trim_positions TRIM_POSITIONS [TRIM_POSITIONS ...]\n                            specify columns to be trimmed from the alignment, e.g.\n                            \"1-10 42\" to trim the first ten columns and the 42th\n                            column\n    --mask [MASK]         mask the alignment instead of trimming. if a character\n                            is specified after --mask, that character will be used\n                            for masking (default char: \"-\")\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flkremer%2Fmsa_trimmer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flkremer%2Fmsa_trimmer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flkremer%2Fmsa_trimmer/lists"}