PredictHaplo statistics

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PredictHaplo specifications

Information


Unique identifier OMICS_00228
Name PredictHaplo
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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Publication for PredictHaplo

PredictHaplo in publications

 (8)
PMCID: 5705913
PMID: 29184023
DOI: 10.1128/mBio.01050-17

[…] at enrollment and 4 years later displayed the expected phylogenetic clustering of sequences in each individual (). we also reconstructed full-length (1,500-bp) viral haplotypes by the use of predicthaplo. the frequency of mutations calculated from reconstructed haplotypes was highly correlated with the frequency of mutations in the raw data, indicating that the reconstruction […]

PMCID: 5822887
PMID: 29492275
DOI: 10.1093/ve/vew022

[…] can be effective, permitting the reconstruction of individual viral variants into ‘haplotypes’ exceeding read length. this problem has been well studied, and tools such as shorah, qure, and predicthaplo () are designed for haplotyping viral populations. shorah () extracts local alignments of a specified window length, reconstructs haplotypes for each ‘cluster’ in that window, […]

PMCID: 4820869
PMID: 27051465
DOI: 10.1186/s13040-016-0090-8

[…] chimeric sequences (exemplified in fig. : method 2). most of the currently available assembly software packages (such as 454’s newbler, celera assembler, clc bio, mira, minimus, vicuna, trinity, predicthaplo, and cufflinks) [, ], were developed for general assembly purposes and have proven to be successful in many ngs studies of diploid/haploid genome assemblies, but their performance […]

PMCID: 4682401
PMID: 26678073
DOI: 10.1186/1471-2105-16-S18-S3

[…] a moderate level of technical sequencing errors., http://sourceforge.net/projects/viquas/ , a number of unsupervised quasispecies spectrum reconstruction (qsr) methods such as shorah [], qure [], predicthaplo [], vispa [] and quasirecomb [] are available in literature. comprehensive reviews on these methods are presented in [] and []. we recently formulated a novel unsupervised method named […]

PMCID: 4227095
PMID: 24996694
DOI: 10.1186/1742-4690-11-56

[…] sequencing errors, are important factors influencing the reliability of haplotype reconstruction. a number of algorithms have been developed for viral haplotype reconstruction [,,,], and among them predicthaplo has been shown to perform at high precision in reconstructing gene haplotypes at a high sequence divergence [,]., we here demonstrate that reconstruction of whole genome hiv-1 haplotypes […]


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PredictHaplo institution(s)
University of Basel, Basel, Switzerland

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