PHYLUCE protocols

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chevron_left Alignment evaluation Genome assembly SNP detection Read alignment Phylogenetic inference Adapter trimming Ultraconserved element detection chevron_right
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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: 4407909
PMID: 25207863
DOI: 10.1111/1755-0998.12328

[…] available from dryad (doi: 10.5061/dryad.46195). computer programs used throughout this study are available from,, and under an open-source, bsd-style licence. sequence reads generated as part of this manuscript are available from the ncbi sequence read […]

PHYLUCE in publications

PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] medical research foundation (oklahoma city, ok) for 150-bp paired-end sequencing on an illumina hiseq3000., to process demultiplexed raw reads for phylogenomic analyses, we followed the standard phyluce pipeline (). illumiprocessor, in combination with trimmomatic, was used to filter low-quality reads and remove adapters (, ), yielding an average of 8,504,473 reads (302,468 to 119,426,985) […]

PMCID: 5895195
PMID: 29732268
DOI: 10.1002/aps3.1038

[…] alignment and phylogenetic reconstruction. several pipelines have been developed to assist: for example, hybpiper (johnson et al., ) was designed for hyb‐seq and exon‐based approaches, whereas phyluce (faircloth, ) was designed for the uce approach. users should pay special attention to the detection of paralogous sequences recovered by sequencing. in some cases, paralogous sequences may […]

PMCID: 5785998
PMID: 29374214
DOI: 10.1038/s41598-018-19946-2

[…] of california, riverside institute for integrative genome biology) or an illumina hiseq. 2500 (brigham young university dna sequencing center)., raw demultiplexed reads were processed with the phyluce pipeline. quality control and adapter removal were conducted with the illumiprocessor wrapper. assemblies were created with velvet and trinity, both at default settings. contigs […]

PMCID: 5699822
PMID: 29166661
DOI: 10.1371/journal.pone.0188044

[…] we performed this step for each of the two sequencing runs, we then concatenated the two different sequencing runs together. after trimming, we generated summary stats on the trimmed reads using the phyluce v1.6 package [], script “phyluce_assembly_get_fastq_lengths”. all programs hereafter beginning with “phyluce” are python programs part of the phyluce package. we assembled the cleaned/trimmed […]

PMCID: 5837689
PMID: 28945862
DOI: 10.1093/sysbio/syx070

[…] of gene a and b., quality filtered raw sequence reads from the uce-enriched libraries were assembled into contigs using the trinity assembler () with a minimum kmer coverage of 2. we used phyluce to identify those assembled contigs that were uce loci. we also harvested uce loci from e. fuscus (gca_000308155.1), myotis brandtii (gca_000412655.1), m. davidii (gca_000327345.1), and m. […]

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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