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Recco specifications

Information


Unique identifier OMICS_27639
Name Recco
Software type Application/Script
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Computer skills Medium
Version 0.93
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Jochen Maydt

Additional information


http://recco.bioinf.mpi-inf.mpg.de/manual.php

Publication for Recco

Recco citations

 (27)
library_books

Tracking HIV 1 recombination to resolve its contribution to HIV 1 evolution in natural infection

2018
Nat Commun
PMCID: 5954121
PMID: 29765018
DOI: 10.1038/s41467-018-04217-5

[…] ics tool to automatically screen for inter-subtype recombinants. More recent and advanced approaches are available today for detection of recombinants and their breakpoints within a single alignment. RECCO finds nominally significant recombinants by comparing the cost of obtaining each sequence either by mutation or by recombination. It does not, however, list parental strains or enumerate distinc […]

library_books

Whole genome diversity of inherited chromosomally integrated HHV 6 derived from healthy individuals of diverse geographic origin

2018
Sci Rep
PMCID: 5823862
PMID: 29472617
DOI: 10.1038/s41598-018-21645-x

[…] culated. Trees were rooted at midpoint, and bootstrap analysis were set at 1000 replicates per tree. The trees were visualized using FigTree. Recombination breakpoint calculations were performed with Recco; genetic identities between predicted recombinant blocks and plots were performed as in Santpere et al.. […]

library_books

Genomic characterization and molecular evolution analysis of subtype B and BF recombinant HIV 1 strains among Argentinean men who have sex with men reveal a complex scenario

2017
PLoS One
PMCID: 5731684
PMID: 29244833
DOI: 10.1371/journal.pone.0189705

[…] Bonferroni correction for multiple comparisons implemented in RDP4) were taken as credible evidence of possible HIV-1 recombination. Lastly, (iii) the recombination analysis using cost optimization (RECCO) was performed. This software computes the number of “savings”, i.e., number of mismatches saved when explaining the read by a recombination event between two viral strains and mutations, rather […]

call_split

Evaluation of Different Parameters of Humoral and Cellular Immune Responses in HIV Serodiscordant Heterosexual Couples: Humoral Response Potentially Implicated in Modulating Transmission Rates

2017
PMCID: 5832641
PMID: 29129698
DOI: 10.1016/j.ebiom.2017.11.001
call_split See protocol

[…] arately for each sequence by following different methods: jumping profile Hidden Markov Model (jpHMM) (), recombination detection program (RDP4) () and recombination analysis using cost optimization (RECCO) (). Subtype was assigned when at least 2 out of 3 methods used were coincident. […]

library_books

Identification of a novel HERV K(HML10): comprehensive characterization and comparative analysis in non human primates provide insights about HML10 proviruses structure and diffusion

2017
Mob DNA
PMCID: 5667498
PMID: 29118853
DOI: 10.1186/s13100-017-0099-7

[…] ng HML9 element could have been erroneously associated to the encompassed HML10 element. To assess this possibility, we analyzed 19p13.2 HML10 with respect to both HML10 and HML9 Dfam references with Recco software [], detecting eventual recombination events among aligned sequences (data not shown). Indeed, an internal portion of the 19p13.2 provirus (from nucleotide 755 to nucleotide 1384, 15% of […]

library_books

Nonstructural Proteins Are Preferential Positive Selection Targets in Zika Virus and Related Flaviviruses

2016
PLoS Negl Trop Dis
PMCID: 5010288
PMID: 27588756
DOI: 10.1371/journal.pntd.0004978

[…] th a critical value (Iss.c). If Iss is significantly lower than Iss.c, sequences have not experienced substitution saturation.The presence of recombination was assessed using two methods, GARD [] and Recco []. Whereas GARD uses phylogenetic incongruence among segments in the alignment to detect the best-fit number and location of recombination breakpoints, Recco is based on cost minimization and d […]

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Recco institution(s)
Max-Planck Institut fur Informatik, Saarbrucken, Germany

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