OGCleaner specifications

Information


Unique identifier OMICS_12828
Name OGCleaner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
SciKit-learn, Aliscore, Pandas, Matplotlib, MAFFT, PAML, Seq-Gen
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Stanley Fujimoto

Publication for OGCleaner

OGCleaner citation

library_books

Overcoming the loss of blue sensitivity through opsin duplication in the largest animal group, beetles

2017
Sci Rep
PMCID: 5428366
PMID: 28127058
DOI: 10.1038/s41598-017-00061-7

[…] cluster represented a single gene and for species with multiple isoforms per gene, only the longest isoform was retained. Clusters were then filtered using a machine-learning algorithm implemented in OGCleaner, to remove low quality putative homology clusters. Alignment quality was assessed using Aliscore (v2.0), and Alicut (v2.0) was used to remove ambiguously aligned positions in the multiple se […]

OGCleaner institution(s)
Computer Science Department, Brigham Young University, Provo, UT, USA; Department of Biology, Brigham Young University, Provo, UT, USA
OGCleaner funding source(s)
This work has been supported by NSF award 1265714 (Phylogenomics, Revisionary Systematics, and Evolution of the Visual Systems in Dragonflies and Damselflies).

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