SiPhy comparative genomics analysis software

SiPhy implements rigorous statistical tests to detect bases under selection from multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as a Hidden Markov Model (HMM), in sliding windows, or to specific regions.

Precomputed genome-wide SiPhy π and ω (in 10-mers) calls for human (genome version GRCh37/hg19) and mouse (GRCm38/mm10) are available here.

SiPhy Sample data

Transcript reconstruction from RNA-Seq

Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. The statistical methods to estimate read coverage significance are also applicable to other sequencing data. Scripture also has modules for ChIP-Seq peak calling.

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Bam2x an Python toolkit for genomic data analysis

Bam2x is a Python library created by Xiaoping Zhu. Bam2x is designed to efficiently access large genomic datasets with minimal memory requirements. It supports most common data formats: Bed, Bam, GTF, Wig, Big Wig. It uses Tabix to index large files.

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