repeatmasker
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
Science Score: 54.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 8 committers (12.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.7%) to scientific vocabulary
Repository
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
Basic Info
- Host: GitHub
- Owner: Dfam-consortium
- License: other
- Language: Perl
- Default Branch: master
- Size: 114 MB
Statistics
- Stars: 269
- Watchers: 5
- Forks: 50
- Open Issues: 16
- Releases: 0
Metadata Files
README.md
``` RepeatMasker Developed by Arian Smit and Robert Hubley Please refer to: Smit, AFA, Hubley, R. & Green, P "RepeatMasker" at http://www.repeatmasker.org
IMPORTANT: The github 'master' branch does not contain any TE libraries. As of 4.1.7, you may use the release as-is for custom library searches (e.g "-lib mylib.fasta"). For searches against community developed TE libraries, you will need to download and install one or more of the Dfam database FamDB partition. See the RepeatMasker website for more information: http://www.repeatmasker.org/RepeatMasker/ ```
RepeatMasker
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). Sequence comparisons in RepeatMasker are performed by one of several available alignment programs: - RMBlast, a variant of NCBI blastn that supports substitution matrices, complexity adjusted scoring and masklevel filtering. - crossmatch, an efficient implementation of the Smith-Waterman-Gotoh algorithm developed by Phil Green. - NHMMER, a profile Hidden Markov Model aligner written by Travis Wheeler and Sean Eddy. - ABBLAST, A blast variant developed by Warren Gish.
See "INSTALL" for instructions on how to install RepeatMasker. See "repeatmasker.help" for a detailed program manual.
Libraries Overview
Updates of the RepeatMasker program are distributed with a copy of the Dfam database ( www.dfam.org ). Dfam is an "open" databases of Transposable Element seed alignments, profile Hidden Markov Models and consensus sequences.
RepeatMasker is also compatible with the RepBase database managed by the Genetic Information Research Institute and requires a license to use. Up until 2019 we maintained the "Repbase RepeatMasker Edition" libraries as co-editor of RepBase Update. For newer versions of RepBase users will need to use the sequences in FASTA format with RepeatMasker's "-lib" option.
RepeatMasker "open-4.0" and later versions are distributed under the Open Source License. Please read LICENSE file for more information.
Owner
- Name: Dfam Consortium
- Login: Dfam-consortium
- Kind: organization
- Email: rhubley@gmail.com
- Website: www.dfam.org
- Repositories: 14
- Profile: https://github.com/Dfam-consortium
Resources for the Study of Transposable Element Families
Citation (CITATION.cff)
cff-version: 1.2.0
title: RepeatMasker
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Arian
family-names: Smit
email: arian.smit@isbscience.org
- given-names: Robert
family-names: Hubley
email: robert.hubley@isbscience.org
repository-code: 'https://github.com/Dfam-consortium/RepeatMasker'
url: 'http://www.repeatmasker.org/'
keywords:
- RepeatMasker
- Transposable Elements
- Genome Annotation
license: OSL-2.1
version: 4.1.8
date-released: '2025-03-12'
GitHub Events
Total
- Issues event: 115
- Watch event: 38
- Issue comment event: 142
- Push event: 19
- Pull request event: 10
- Fork event: 1
Last Year
- Issues event: 115
- Watch event: 38
- Issue comment event: 142
- Push event: 19
- Pull request event: 10
- Fork event: 1
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Robert Hubley | r****y@s****g | 159 |
| Jeb Rosen | j****n@i****g | 25 |
| Robert Hubley | r****y@g****m | 7 |
| Mark Diekhans | m****d@u****u | 2 |
| Mitchell Robert Vollger | m****r@g****m | 1 |
| Michael Beavitt | m****t@g****m | 1 |
| Daniel García Ruano | d****e@g****m | 1 |
| asgray | a****9@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 59
- Total pull requests: 7
- Average time to close issues: 2 months
- Average time to close pull requests: about 1 month
- Total issue authors: 49
- Total pull request authors: 3
- Average comments per issue: 2.0
- Average comments per pull request: 0.43
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 58
- Pull requests: 7
- Average time to close issues: 2 months
- Average time to close pull requests: about 1 month
- Issue authors: 48
- Pull request authors: 3
- Average comments per issue: 2.02
- Average comments per pull request: 0.43
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Adamtaranto (5)
- jayoung (4)
- jebrosen (3)
- ohan-Bioinfo (2)
- minhasbushra (2)
- DryadDataDiver (2)
- Zhenlisme (2)
- BioFalcon (2)
- kuangtianhui (2)
- 0xaf1f (2)
- KirillKryukov (2)
- manighanipoor (2)
- meduri-ruthwick (2)
- ltswx (1)
- nealsongs (1)
Pull Request Authors
- rmhubley (6)
- Windyxia11 (2)
- bhdobrin (1)
- tzvi909 (1)
- manighanipoor (1)
- dgruano (1)
- kavonrtep (1)
- asgray (1)