PHYLUCE pipeline

PHYLUCE specifications


Unique identifier OMICS_10301
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Java, Python
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.6.6
Stability Stable
Maintained Yes


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  • person_outline Brant C. Faircloth <>

Publication for PHYLUCE

PHYLUCE IN pipeline

PMCID: 4759850
PMID: 26896057
DOI: 10.1186/s12862-016-0611-6

[…] divergence (or two nucleotide positions, whatever was greater) were present in a sample for any given uce locus, trinity retained the allele supported by the largest number of reads. we used phyluce v. 1.4 (faircloth et al. [25, 30]) to match contigs to uce loci and generated two alignments in mafft [31]: one containing no missing loci across all individuals (complete) and another […]

PHYLUCE institution(s)
Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
PHYLUCE funding source(s)
Supported by the National Science Foundation Division of Environmental Biology (grant numbers DEB-1242260, DEB-0956069, DEB0841729, DEB-1354739) and start-up funds provided by Louisiana State University.

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