HAPLOFIND protocols

View HAPLOFIND computational protocol

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HAPLOFIND specifications

Information


Unique identifier OMICS_07996
Name HAPLOFIND
Interface Web user interface
Restrictions to use None
Input data Sequences
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline Dario Vianello <>

Publication for HAPLOFIND

HAPLOFIND in pipeline

2017
PMCID: 5724682
PMID: 28884802
DOI: 10.1002/ajpa.23308

[…] in mitochondrial sequences (green et al., ). the consensus mitochondrial dna (mtdna) sequences were called using samtools package (li et al. ) while the initial haplogroup assignment was in haplofind tool (vianello et al., ). the assignments were inspected manually by checking against phylotree–mtdna tree build 17 (18 february 2016) (van oven & kayser, ). for details consult […]


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HAPLOFIND in publications

 (20)
PMCID: 5902838
PMID: 29661137
DOI: 10.1186/s12864-018-4593-1

[…] in this study., all haplotypes of 1092 individuals, putative cases of gene conversion and local gc content of putative gene conversion sites were obtained with our pipeline of five perl programs (haplofind.pl, geneconversionfind.pl, bgc_calculator.pl, localgc_calculator.pl, at_vs_gc.pl, randomgc_calculator.pl). detailed description and scripts of all our perl programs, their instruction […]

PMCID: 5851556
PMID: 29538439
DOI: 10.1371/journal.pone.0193578

[…] []. the latter one was also executed for the reconstruction of endogenous mitochondrial genomes. classification of complete mtdna sequences according to haplogroup nomenclature was achieved using haplofind []., molecular analyses for another subset of samples (m1, m3, m4, and m5) were replicated by another independent research group at the department of genetics, physical anthropology […]

PMCID: 5879675
PMID: 29531053
DOI: 10.1073/pnas.1717762115

[…] adna damage, and for samples with high levels of mitochondrial contamination (>15%), the analysis was restricted to fragments indicating postmortem damage (). see si appendix, section s4., haplofind () was used to infer the most likely haplogroup for mitochondrial consensus sequences. y chromosomal haplogroups were assigned by investigating up to 732 haplotype-informative single base […]

PMCID: 5802798
PMID: 29410482
DOI: 10.1038/s41598-018-20705-6

[…] 16033–16365 np, and hvs-ii 73–340 np) (supplementary table ). π was calculated for the fragment of mtdna hvs-i region (16000–16410 np) (supplementary table )., haplogroups were predicted with haplofind with respect to phylotree build 17 (http://www.phylotree.org/). only samples with a haplogroup score ≥ 0.8 and average coverage ≥ 3 were used in downstream analyses. to assess temporal […]

PMCID: 5727115
PMID: 29234095
DOI: 10.1038/s41598-017-17728-w

[…] errors, were trimmed from the final alignment used in the analysis. sequence alignments, including the rsrs sequence, were assembled with mafft v7.123b., haplogroup assignment was performed with haplofind and haplogrep 2, and manually confirmed by checking diagnostic positions as described in phylotree v.17. haplogrep was also used to list the polymorphisms in each sample, as included […]


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HAPLOFIND institution(s)
Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy

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