| NCBI | National Center for Biotechnology Information Search database. |
| RIGW | Rice Information GateWay. |
| Ensembl | Ensembl is a genome browser for vertebrate genomes. |
| PACBIO | Pacific Biosciences provides sophisticated genomic analysis systems. |
| agriGO | The agriGO is a web-based tool and database for the gene ontology analysis. |
| InterProScan | InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. |
| SMART | SMART allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. |
| Superfamily | Superfamily is a database of structural and functional annotation for all proteins and genomes. |
| ExPASy | ExPASy is the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools. |
| EMBL-EBI | EBI Search is a scalable text search engine that provides easy and uniform access to the biological data resources hosted at the (EMBL-EBI) |
| Cogent | version: 3.5 | COding GENome reconstruction Tool. |
| SMRT Tools | version: 5.0.1 | Analyze, visualize, and manage SMRT-data through command-line interface. |
| SUPPA | version: 2.0 | SUPPA is a tool to study splicing at the transcript isoform or at the local alternative splicing event level. |
| TAPIS | version: 2017-12-03 | Transriptome Analysis Pipeline from Isoform Sequencing. |
| Gbrowse | version: 2.54 | GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. |
| LoRDEC | version: 0.7 | A hybrid error correction program for long, PacBio reads. |
| GMAP | version: 2017-11-15 | A Genomic Mapping and Alignment Program for mRNA and EST Sequences. |
| InterProScan | version: 5.30 | InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. |
| ORFfinder | ORF finder searches for open reading frames (ORFs) in the DNA sequence you enter. | |
| pipeline-for-isoseq | A pipeline quote from [Wang, M., et al.] which can be used to analysis Iso-Seq data of G.barbadense. | |
| alternative_splice.py | A Python program which can detect AS event. | |
| SQANTI | An automated pipeline for the classification of long-read transcripts that can assess the quality of data. |
| A.membranaceus | Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript etc. |
| A.thaliana | cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing. |
| A.trichopoda | Detecting Alternatively Spliced Transcript Isoforms from Single-Molecule Long-Read Sequences without a Reference Genome. |
| B.vulgaris subsp. vulgaris | Exploiting single-molecule transcript sequencing for eukaryotic gene prediction. |
| C.arabica | Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts. |
| F.vesca | Global identification of alternative splicing via comparative analysis of SMRT‐ and Illumina‐based RNA‐seq in strawberry. |
| G.barbadense | A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation. |
| H.brasiliensis | De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species. |
| Nepenthes | Iso-Seq analysis of Nepenthes ampullaria, Nepenthes rafflesiana and Nepenthes÷hookeriana for hybridisation study in pitcher plants. |
| P.edulis | Comprehensive profiling of rhizome-associated alternative splicing and alternative polyadenylation in moso bamboo etc. |
| P.ginseng | Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome. |
| S.bicolor | A survey of the sorghum transcriptome using single-molecule long reads. |
| T.aestivum | An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. |
| Z.mays | Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. |
| A.thaliana | Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. |
| A.trichopoda | The Amborella Genome and the Evolution of Flowering Plants. |
| B.vulgaris subsp. vulgaris | The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). |
| C.arabica | Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content. |
| C.quinoa | A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance etc. |
| F.vesca | Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing. |
| G.barbadense | Rapid evolutionary divergence of Gossypium barbadense and G. hirsutum mitochondrial genomes. |
| H.brasiliensis | The rubber tree genome reveals new insights into rubber production and species adaptation. |
| P.edulis | The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). |
| P.ginseng | Panax ginseng genome examination for ginsenoside biosynthesis. |
| S.bicolor | Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). |
| T.aestivum | A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. |
| Z.mays | Improved maize reference genome with single-molecule technologies. |
| Pictures | You can gain our pictures of species by searching them on wikipedia. |