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SEQLinkage specifications

Information


Unique identifier OMICS_09407
Name SEQLinkage
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format VCF
Operating system Unix/Linux
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Suzanne Leal <>

Publication for SEQLinkage

SEQLinkage in publications

 (8)
PMCID: 5862535
PMID: 29522508
DOI: 10.1371/journal.pgen.1007239

[…] the 16s ribosomal rna sequences of all genomes. pair wise distances were calculated using the distance model by jukes and cantor [] and the blosum62 scoring matrix. the tree was constructed with the seqlinkage function by matlab using the default parameters. as expected, the only non-photosynthetic organism e. coli appears as an outgroup., identification of orthologous genes was done […]

PMCID: 5510992
PMID: 28715588
DOI: 10.1167/iovs.16-21271

[…] included in the pruning; they were retained due to their high information level and general low intermarker ld with nearby snps., collapsed haplotype pattern (chp) variants were created using the seqlinkage software. this program uses rare variants to create short regional haplotypes that serve as multiallelic pseudo-markers corresponding to specific genetic regions such as genes (determined […]

PMCID: 5302377
PMID: 28187204
DOI: 10.1371/journal.pone.0171572

[…] multiple alignment method (multialign). pairwise distances were calculated with the jukes-cantor method, with the phylogenetic tree generated using the unweighted pair group method average (seqlinkage). aa positions in the aligned sequences were numbered relative to hxb2 according to the convention of korber et al. []., env was sequenced from an additional set of subtype b virus for 5 […]

PMCID: 5297824
PMID: 28106787
DOI: 10.3390/ijms18010193

[…] linkage method, we plot several phylogenetic trees for the mirnas and viruses (or bacteria), based on different distance methods and the linkage methods, respectively. two matlab codes, seqpdist and seqlinkage, are used to plot the trees. for the mirna phylogenetic trees, is the tree based on the juke–cantor distance and single linkage function; is the tree based on alignment score distance […]

PMCID: 4977546
PMID: 27502179
DOI: 10.1038/srep31326

[…] representative ancient samples, and different modern populations from the same geographic area as gd13a, and generated an unweighted pair group method with arithmetic mean (upgma) tree using the seqlinkage function in matlab’s bioinformatics toolbox., in order to examine runs of homozygosity (roh) we used imputation to infer diploid genotypes in our sample following the method described […]


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SEQLinkage institution(s)
Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA

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