PineSAP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PineSAP
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Tool usage distribution map

This map represents all the scientific publications referring to PineSAP per scientific context
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Protocols

PineSAP specifications

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Unique identifier OMICS_10360
Name PineSAP
Alternative name Pine Alignment and SNP Identification Pipeline
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained No

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Publication for Pine Alignment and SNP Identification Pipeline

PineSAP citations

 (3)
library_books

Micro and Macro Geographic Scale Effect on the Molecular Imprint of Selection and Adaptation in Norway Spruce

2014
PLoS One
PMCID: 4281139
PMID: 25551624
DOI: 10.1371/journal.pone.0115499

[…] edu/NealeLab/crsp/overview.php). DNA was extracted from the haploid megagametophyte, obtained from one seed per sampled tree. Individual sequence alignment and SNP identification were performed using PineSAP . A final set of 384 SNPs among those having quality design scores above 0.6, were selected for the genotyping, considering a maximum of two SNPs per locus, and preferring SNPs determining a c […]

call_split

An empirical evaluation of two stage species tree inference strategies using a multilocus dataset from North American pines

2014
BMC Evol Biol
PMCID: 4021425
PMID: 24678701
DOI: 10.1186/1471-2148-14-67
call_split See protocol

[…] ducts amplified from haploid megagametophyte tissue excised from seeds of each species. Further description of laboratory protocols appears in []. Sequence data were pre-processed and organized using PINESAP[], a bioinformatics pipeline that combines PHRED[], PHRAP[], and MUSCLE[,] to call bases and align sequencing reads. Reported nucleotide sequences consisted only of A, C, G, T, missing, and ga […]

call_split

Contrasting patterns of nucleotide diversity for four conifers of Alpine European forests

2012
Evol Appl
PMCID: 3492901
PMID: 23144662
DOI: 10.1111/j.1752-4571.2012.00256.x
call_split See protocol

[…] A customized pipeline, PineSAP (), was used to generate sequence alignments and to identify SNPs. A customized Perl script (https://dendrome.ucdavis.edu/TGPlone/research-projects/ace-sap/) was used subsequently to identify […]


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PineSAP institution(s)
Department of Plant Sciences, University of California, Davis, CA, USA
PineSAP funding source(s)
Association Genetics of Natural Genetic Variation and Complex Traits in Pine – NSF 0501763

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