Tools

Assembly

Genome-organization-framework Assisted Assembly Pipeline(GAAP)

GAAP is aimed at scaffolding and extending scaffolds and contigs based on de novo assembly of one paired-end library and core gene cluster from multiple related references.

GOBOND: A stand-alone accurate scaffolding program

GOBOND, which is a stand-alone scaffolding program with more accuracy to deal with complicated genome. It is the bridge to join together the data from multiple platforms.Pre-assembled contigs from one sequencing platform could be oriented and linked by pair-end/mate-pair reads from other platforms.

Evolution

Genome-organization-framework Assisted Assembly Pipeline(GAAP)

GAAP is aimed at scaffolding and extending scaffolds and contigs based on de novo assembly of one paired-end library and core gene cluster from multiple related references.

EvolView: A revolutionized approach to visualize phylogenetic trees

EvolView is an easy-to-use online tool for displaying, managing and customizing phylogenetic trees. EvolView provides a WYSIWYG (What-You-See-Is-What-You-Get) editor and a desktop-like web interface.

KaKs_Calcultor: calculating nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging

KaKs_Calculator adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences.

Methylation

BS-RNA: a novel mapping and annotation tool for RNA bisulfite sequencing data

BS-RNA can analyze RNA methylation for bisulfite sequencing data. Evaluation results of the rates of uniquely mapped reads, rates of correctly mapped reads, and running time for simulated data and actual data indicate that BS-RNA can provide fast and accurate mapping of RNA bisulfite sequencing reads.

MeRIP-Seq Peak-Finding Program

MeRIP-PF, a high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads generated by high-throughput sequencing technologies between immunoprecipitation sample and control sample.

WBSA: Web service for Bisulfite Sequencing data Analysis

WBSA is a free web service for analysis of Whole-Genome Bisulfite-Sequencing (WGBS) and Genome-wide Reduced Representation Bisulfite Sequencing (RRBS) data.

Pangenome

Genome-organization-framework Assisted Assembly Pipeline(GAAP)

GAAP is aimed at scaffolding and extending scaffolds and contigs based on de novo assembly of one paired-end library and core gene cluster from multiple related references.

Sequence Analysis

Composition Analysis Toolkit (CAT)

CAT is a software package that includes a novel measure of codon usage bias, Codon Deviation Coefficient. Unlike previous measures, CDC effectively accounts for background nucleotide composition in estimating codon usage bias and utilizes a bootstrap assessment of the statistical significance of codon usage bias.

KaKs_Calcultor: calculating nonsynonymous (Ka) and synonymous (Ks) substitution rates through model selection and model averaging

KaKs_Calculator adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences.

ParaAT

ParaAT is a parallel tool that parallelly constructs protein-coding DNA alignments for a large number of homologs. ParaAT is well suited for large-scale data analysis in the high-throughput era, providing good scalability and exhibiting high parallel efficiency for computationally demanding tasks.

Transcriptome Profiling

BS-RNA: a novel mapping and annotation tool for RNA bisulfite sequencing data

BS-RNA can analyze RNA methylation for bisulfite sequencing data. Evaluation results of the rates of uniquely mapped reads, rates of correctly mapped reads, and running time for simulated data and actual data indicate that BS-RNA can provide fast and accurate mapping of RNA bisulfite sequencing reads.

MeRIP-Seq Peak-Finding Program

MeRIP-PF, a high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads generated by high-throughput sequencing technologies between immunoprecipitation sample and control sample..

wapRNA: A web-based application for the processing of RNA sequence

wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content.

WBSA: Web service for Bisulfite Sequencing data Analysis

WBSA is a free web service for analysis of Whole-Genome Bisulfite-Sequencing (WGBS) and Genome-wide Reduced Representation Bisulfite Sequencing (RRBS) data.