Pecan specifications


Unique identifier OMICS_03739
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 <>

Pecan articles

Pecan citation

PMCID: 3245118

[…] 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 […]

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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