SiPhy protocols

SiPhy specifications

Information


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.
Input format FASTA,MAF,PHYLIP
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 0.5
Stability Stable
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Versioning


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Maintainer


  • person_outline Xiaohui Xie <>

Publication for Site-specific PHYlogenetic analysis

SiPhy IN pipelines

 (4)
2016
PMCID: 4968975
PMID: 27493474
DOI: 10.4137/EBO.S37594

[…] 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., […]

2016
PMCID: 4968975
PMID: 27493474
DOI: 10.4137/EBO.S37594

[…] 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., we used pairwise alignments from ucsc genome browser37 to analyze the evolutionary dynamics of rna […]

2013
PMCID: 3552696
PMID: 23369519
DOI: 10.1186/1755-8794-6-S1-S7

[…] by the total number of sequencing reads falling into the lincrna exonic regions. rpkm values were calculated for each lincrna., we calculated the conservation score across placental mammals using siphy [62] on various genomic regions, including exons and introns for protein coding genes, lincrna exons and introns, random genomic regions, and predicted mirna binding sites on lincrnas. we used […]

2013
PMCID: 3552696
PMID: 23369519
DOI: 10.1186/1755-8794-6-S1-S7

[…] random genomic regions, and predicted mirna binding sites on lincrnas. we used the ω  as the conservation score, which models the overall mutation rates across placental mammals [42]. the input of siphy is a multiple alignment file (maf) and a placental mammals model file. all known gene annotations (refseq), genome sequences (hg18 and mm9), liftover tool, multiple alignment files, […]

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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