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Protocols

COCO-CL specifications

Information


Unique identifier OMICS_05364
Name COCO-CL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Raja Jothi

Publication for COCO-CL

COCO-CL citations

 (10)
library_books

New Tools in Orthology Analysis: A Brief Review of Promising Perspectives

2017
Front Genet
PMCID: 5674930
PMID: 29163633
DOI: 10.3389/fgene.2017.00165

[…] arkov Cluster Algorithm models of the Basic Alignment Search Tool (BLAST) algorithm (Chen et al., ); of Reciprocal Best Hits (RBH) (Zielezinski et al., ); of Correlation Coefficient-based Clustering (COCO-CL), COCO-CL (Raja et al., ); of Automatic Clustering of Orthologs and In-paralogs (InParanoid) (O'Brien, ) leading to the appearance of various tools such as the a Markov Cluster algorithm for g […]

library_books

A comparative genomic analysis of putative pathogenicity genes in the host specific sibling species Colletotrichum graminicola and Colletotrichum sublineola

2017
BMC Genomics
PMCID: 5225507
PMID: 28073340
DOI: 10.1186/s12864-016-3457-9

[…] nual analysis of the genes located on either side of the “backbone” SSM-associated genes (ie. the genes encoding PKS, NRPS, TS, DMAT, and PKS-NRPS hybrids) that had been identified by using Ortho-MCL/COCO-CL and Pfam. A total of 67 putative SSM-associated gene clusters in the C. sublineola genome (Additional file : Table S6), were compared with the 42 clusters that were previously identified from […]

library_books

Inferring Orthologs: Open Questions and Perspectives

2016
PMCID: 4778853
PMID: 26966373
DOI: 10.4137/GEI.S37925

[…] rely on merging gene and species phylogeny to determine the subset of orthologs: Orthostrapper, RIO, PhIGs, PhyOP, TreeFam, LOFT, EnsemblCompara GeneTrees based on TreeBeST method, SYNERGY, and PHOG. COCO-CL is based on a hierarchical clustering algorithm of correlated genes guided by phylogenetic relationships. Species phylogeny was originally based on rRNA genes, and with the availability of com […]

call_split

BIR Pipeline for Preparation of Phylogenomic Data

2015
Evol Bioinform Online
PMCID: 4412416
PMID: 25987827
DOI: 10.4137/EBO.S10189
call_split See protocol

[…] eline, but other options can be used in a separate installation of RAxML on Lifeportal. In the last step of the pipeline, orthologous groups of sequences are predicted by hierarchical clustering with COCO-CL. This algorithm requires a similarity distance matrix that is calculated separately using ClustalW. The pipeline provides alignments for users who want to use other bioinformatic tools or tree […]

library_books

Quantitative synteny scoring improves homology inference and partitioning of gene families

2013
BMC Bioinformatics
PMCID: 3852004
PMID: 24564516
DOI: 10.1186/1471-2105-14-S15-S12

[…] next generation of homology inference algorithms improved the accuracy and the time and/or memory complexity requirements and include algorithms like Neighborhood Correlation [], HiFiX [], PHYRN [], COCO-CL [] etc. and infer homologs by extracting evidence from network structure of BLAST hits or multiple sequence alignments.The algorithms mentioned previously are all based on sequence similarity. […]

library_books

Plant Symbiotic Fungi as Chemical Engineers: Multi Genome Analysis of the Clavicipitaceae Reveals Dynamics of Alkaloid Loci

2013
PLoS Genet
PMCID: 3585121
PMID: 23468653
DOI: 10.1371/journal.pgen.1003323

[…] -bio , MCL version 10–201 (http://micans.org/mcl/) , and NCBI BLAST version 2.2.25 .As noted by Li et al. , an OrthoMCL-derived “ortholog group” may contain paralogs as well as orthologs. We used the COCO-CL software distribution to recursively divide the ortholog groups obtained from OrthoMCL into sub-groups. A division was accepted if it had a bootstrap score of 0.75 or greater and a split-scor […]

Citations

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COCO-CL institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

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