SiPhy pipeline

SiPhy specifications


Unique identifier OMICS_00183
Name SiPhy
Alternative name Site-specific PHYlogenetic analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some alignment files.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 0.5
Stability Stable
Maintained Yes


  • Animals
    • Homo sapiens


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  • person_outline Xiaohui Xie <>

Publication for Site-specific PHYlogenetic analysis

SiPhy citations

PMCID: 5125825

[…] which included 150 files in k562 cells and 77 for hepg2 cells. the conserved elements were the hg19 liftover of the siphy-pi65 conserved elements from ref. 42. the repeats were based on repeatmasker70 obtained through the ucsc genome browser71., the motif analysis comparing k562 and hepg2 cells (fig. 4, […]

PMCID: 4968975

[…] enrichment analysis using the kegg orthology-based annotation system (kobas).35, to assess the conservation level of each lincrna and protein-coding gene, site-specific phy-logenetic analysis (siphy)36 was run on the 46-way alignment available from ucsc genome browser.37 the omega value from siphy calculation36 was used to evaluate nucleotide sequence conservation throughout this study., […]

SiPhy institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biology, MIT, Cambridge, MA, USA; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden; School of Computer Science and Engineering, Institute of Life Sciences, Hebrew University, Jerusalem, Israel; Department of Computer Science, Institute for Genomics and Bioinformatics, University of California, Irvine, CA, USA
SiPhy funding source(s)
Supported by UCI, NHGRI and Israel Science Foundation.

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