PineSAP statistics

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Citations per year

Number of citations per year for the bioinformatics software tool PineSAP

Tool usage distribution map

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


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


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

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 […]


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

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 […]


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

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 ( 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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