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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

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Maintainer


  • person_outline Raja Jothi <>

Publication for COCO-CL

COCO-CL in pipeline

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

[…] were the fgenesh gene predictions previously used in the clavicipitaceae analysis []. putative orthologs were identified by using two methods. the first method was application of ortho-mcl and coco-cl (correlation coefficient-based clustering) to the annotations [, ], following a procedure previously used for ortholog identification within the clavicipitaceae []. the species included […]


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COCO-CL in publications

 (6)
PMCID: 5225507
PMID: 28073340
DOI: 10.1186/s12864-016-3457-9

[…] []. similar categories of cazymes were also evolving rapidly among a larger group of more distantly related genera of colletotrichum fungi [, ]., the program ortho-mcl and the refiner coco-cl were used to identify genes in c. sublineola that were orthologous to the previously identified ssm-associated genes of c. graminicola and c. higginsianum []. using this approach, combined […]

PMCID: 4412416
PMID: 25987827
DOI: 10.4137/EBO.S10189

[…] 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 […]

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 […]

PMCID: 3544860
PMID: 23342000
DOI: 10.1371/journal.pone.0053786

[…] genomes only and roundup computes pairs of orthologs only, i.e. there is no further grouping . to our knowledge, the only graph-based algorithm for hierarchical group inference published to date is coco-cl , which despite its pioneering character is a somewhat ad-hoc approach. indeed coco-cl can be shown to return suboptimal results on relatively simple problems, even with perfect input data […]

PMCID: 3283307
PMID: 22151970
DOI: 10.1186/1471-2105-12-S9-S18

[…] with the previously defined and expert validated orthologous subgroups []. we have compared the orthologous groups obtained by syns on the yeast data to those obtained by the following methods: coco-cl [], multiparanoid [] and orthomcl []. table shows the numbers of orthologous groups classified by these methods. orthomcl [] was run with default inflation index= 1.5, e-value cut-off= –5 […]


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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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