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Pecan specifications


Unique identifier OMICS_03739
Name Pecan
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Output data A file containing a formatted alignment.
Output format FASTA
Operating system Unix/Linux
Programming languages Java, Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained No




No version available



This tool is not available anymore.

Publications for Pecan

Pecan citations


Large scale variation in the rate of germ line de novo mutation, base composition, divergence and diversity in humans

PLoS Genet
PMCID: 5891062
PMID: 29590096
DOI: 10.1371/journal.pgen.1007254

[…] (ii) the UCSC MultiZ (MZ) 46-way alignments [] downloaded from and (iii) Ensembl Enredo, Pecan, Ortheus (EPO) 6 primate multiple alignment, release 74, [] downloaded from We found that the EPO alignments were the mos […]


Identification of candidate protective variants for common diseases and evaluation of their protective potential

BMC Genomics
PMCID: 5543444
PMID: 28774272
DOI: 10.1186/s12864-017-3964-3

[…] inferred from whole genome alignments of 6 primate species (H. sapiens, P. troglodytes, G. gorilla, P. pygmaeus, M. mulatta and C. jacchus) released in Ensembl Compara 59 which implemented the Enredo-Pecan-Ortheus (EPO) alignment method []. We accessed this information from phase 1 of the 1000 Genomes project [] by applying the tabix command from the SAM tools package [] to the relevant chromosome […]


Survey of cryptic unstable transcripts in yeast

BMC Genomics
PMCID: 4845318
PMID: 27113450
DOI: 10.1186/s12864-016-2622-5
call_split See protocol

[…] We used Pecan version 0.9 [, ] to generate a four-way whole genome multiple sequence alignment of the S288c, Σ1278b, JAY291, and N17 genomes. As the JAY291 genome is currently only available in a contig assem […]


Ensembl comparative genomics resources

PMCID: 4761110
PMID: 26896847
DOI: 10.1093/database/bav096

[…] election of pairs of species. It is also worth noting that these syntenic blocks are not intended to show duplications in one species with respect to another. Duplications are presented in the Enredo-Pecan-Ortheus (EPO) whole-genome alignments (, ) which specifically support such features and are described below. […]


Inter population Differences in Retrogene Loss and Expression in Humans

PLoS Genet
PMCID: 4608704
PMID: 26474060
DOI: 10.1371/journal.pgen.1005579

[…] Orthologs of human retrocopies in 13 other eutherian species were identified using Amniota vertebrates PECAN [] whole genome alignment from Ensembl release 73 [], requiring a reciprocal overlap of at least 50% between retrocopy sequences from different organisms in the alignment. To be more specific, w […]


The interplay between DNA methylation and sequence divergence in recent human evolution

Nucleic Acids Res
PMCID: 4787803
PMID: 26170231
DOI: 10.1093/nar/gkv693

[…] ustom Perl scripts were used to summarize the methylation levels of individual cytosines based on frequency of mapped reads.To facilitate an unbiased comparison of the four genomes we used the Enredo-Pecan-Orthus (EPO) whole-genome multiple alignments of human, chimpanzee, gorilla and orangutan [Ensemble Compara.6_primates_EPO] (). We identified 8,952,000 CpG positions shared among the four specie […]


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Pecan institution(s)
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA, USA; EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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