Pecan pipeline

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
Requirements Exonerate
Maintained Yes



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  • person_outline Benedict Paten <>

Publications for Pecan

Pecan IN pipelines

PMCID: 3764194
PMID: 24039605
DOI: 10.1371/journal.pgen.1003763

[…] probes shared between human and chimpanzee., to investigate the global correspondence of dna sequence differences between species and the degree of methylation changes, we examined the enredo-pecan-orthus (epo) whole-genome multiple alignments of human, chimpanzee, gorilla, and orangutan [ensemble compara.6_primates_epo] [28], [29]. considering only those blocks with alignments […]

PMCID: 3245118
PMID: 22067447
DOI: 10.1093/nar/gkr895

[…] dna sequences, using the tools lastz (15) and (for more diverged genomes) translated blat (16), combined with the use of the ucsc chain/net algorithm (17); and multiple alignments using enredo and pecan (18). protein alignments are used to reconstruct evolutionary trees for related genes using the ensembl compara gene trees pipeline (19). these are run for each individual domain […]

PMCID: 2885371
PMID: 20459813
DOI: 10.1186/1471-2105-11-240

[…] communication method., over time, we will want to change some parts of our pipeline. for instance, multi-lagan [20] was used in our pipelines to build multiple alignments before the deployment of pecan [14]. similarly, our most current analysis pipeline uses enredo [14] rather than mercator [12], and we have recently added ortheus to our multiple alignment pipeline to infer ancestral genomic […]

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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