+ Site Statistics
+ Search Articles
+ Subscribe to Site Feeds
EurekaMag Most Shared ContentMost Shared
EurekaMag PDF Full Text ContentPDF Full Text
+ PDF Full Text
Request PDF Full TextRequest PDF Full Text
+ Follow Us
Follow on FacebookFollow on Facebook
Follow on TwitterFollow on Twitter
Follow on LinkedInFollow on LinkedIn

+ Translate

PHYLUCE is a software package for the analysis of conserved genomic loci

PHYLUCE is a software package for the analysis of conserved genomic loci

Bioinformatics 32(5): 786-788

Targeted enrichment of conserved and ultraconserved genomic elements allows universal collection of phylogenomic data from hundreds of species at multiple time scales (<5 Ma to > 300 Ma). Prior to downstream inference, data from these types of targeted enrichment studies must undergo preprocessing to assemble contigs from sequence data; identify targeted, enriched loci from the off-target background data; align enriched contigs representing conserved loci to one another; and prepare and manipulate these alignments for subsequent phylogenomic inference. PHYLUCE is an efficient and easy-to-install software package that accomplishes these tasks across hundreds of taxa and thousands of enriched loci.Label="AVAILABILITY AND IMPLEMENTATION">PHYLUCE is written for Python 2.7. PHYLUCE is supported on OSX and Linux (RedHat/CentOS) operating systems. PHYLUCE source code is distributed under a BSD-style license from PHYLUCE is also available as a package ( for the Anaconda Python distribution that installs all dependencies, and users can request a PHYLUCE instance on iPlant Atmosphere (tag: phyluce). The software manual and a tutorial are available from and test data are available from doi: 10.6084/m9.figshare.1284521.Label="CONTACT">brant@faircloth-lab.orgLabel="SUPPLEMENTARY INFORMATION">Supplementary data are available at Bioinformatics online.

(PDF emailed within 0-6 h: $19.90)

Accession: 058493485

Download citation: RISBibTeXText

PMID: 26530724

DOI: 10.1093/bioinformatics/btv646

Related references

Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing. Bmc Bioinformatics 11(): 572-572, 2011

Using the RNAstructure Software Package to Predict Conserved RNA Structures. Current Protocols in Bioinformatics 46: 12.4.1-22, 2016

Hardware and software design considerations in engineering and image processing workstation autoradiographic analysis with dumas and the brain autoradiograph analysis software package. Mceachron, D L (Ed ) Experimental Biology And Medicine, Vol 11 Functional Mapping in Biology And Medicine: Computer Assisted Autoradiography; Drexel University Workshop, Philadelphia, Pennsylvania, Usa, May 28-31, 1985 Viii+278p S Karger Ag: Basel, Switzerland; New York, New York, Usa Illus 175-201, 1986, 1987

GenoMatrix: A Software Package for Pedigree-Based and Genomic Prediction Analyses on Complex Traits. Journal of Heredity 107(4): 372-379, 2016

Genomic sequence analysis of the CTLA4/ICOS gene loci Structural features are conserved between human and mouse ICOS receptors. Faseb Journal. 14(6): A1169, Il 20, 2000

Software for selecting the most informative sets of genomic loci for multi-target microbial typing. Bmc Bioinformatics 14(): 148-148, 2013

Survival analysis using SAS software package. Zhong Xi Yi Jie He Xue Bao 8(5): 489-493, 2012

A software package for geostatistical analysis. Memorias del XI congreso Latinoamericano y II congreso Cubano de la ciencia del suelo, 11-17 de Marzo 1990, La Habana, Cuba Volumen II: genesis, clasificacion y cartografia de suelos recursos hidricos, 11-17 Marzo 1990, La Habana, Cuba: 515-518, 1993

Conserved genomic structure of the Cyp1a1 and Cyp1a2 loci and their dioxin responsive elements cluster. Biochemical Pharmacology 77(4): 654-659, 2008

Principal component analysis and exploratory factor analysis using SAS software package. Zhong Xi Yi Jie He Xue Bao 8(6): 589-593, 2012

MIBPB: a software package for electrostatic analysis. Journal of Computational Chemistry 32(4): 756-770, 2011

Software package for structure analysis of quasicrystals. Science and Technology of Advanced Materials 9(1): 013001-013001, 2008

PEPPLOTT, a protein secondary structure analysis program for the UWGCG sequence analysis software package. Nucleic acids research, 14(1): 327-334, 1986

The UNAIDS Estimation and Projection Package: a software package to estimate and project national HIV epidemics. Sexually Transmitted Infections 80 Suppl 1: I5-I9, 2004