AGRP
Asteraceae Genomic Research Platform
Asteraceae Genomic Research Platform
Bio-informatics Utilities Platform
| No. | Tool Name ↕ | Usage Count ↓ | Description |
|---|---|---|---|
| 1 | B_Dotter *🔥 | 5 | Self-developed blastp dot plot function. |
| 2 | Blast🔥 | 4 | Call the blast software to perform sequence alignment to arbitrary files. |
| 3 | BBK_Dotter *🔥 | 4 | Self-developed ks dot plot function. |
| 4 | KaKs_Calculator🔥 | 3 | Call KaKs Calculator to calculate KaKs, integrating a variety of algorithms (NG86, YN00, MYN, LWL85, etc.). |
| 5 | BB_Dotter *🔥 | 3 | Self-developed function of drawing block dot plots. |
| 6 | Diamond🔥 | 2 | Call the Diamond software for sequence alignment, arbitrary files. |
| 7 | Blast match *🔥 | 2 | Leguminosae sequence alignment and best match. |
| 8 | Sequence fetch *🔥 | 2 | Find cds and pep sequences for gene ids. |
| 9 | Dupgen finder🔥 | 2 | The Dupgen finder software is invoked to analyze the type of gene replication. |
| 10 | Sequenceserver🔥 | 1 | Leguminosae sequence alignment and Matching visualization. |
| 11 | MCScanX | 1 | Calls MCScanX software to perform collinearity analysis on arbitrary files. |
| 12 | ColinearScan | 1 | Calls the ColinearScan software to perform collinearity analysis on any file. |
| 13 | Syntenic visualization | 1 | A collinear visualization implemented by the invoked Synvisio software based on the results of MCScanX. |
| 14 | Block number count * | 0 | Generates the block statistics result based on the ColinearScan result file. |
| 15 | ParaAT | 0 | Call ParaAT to calculate KaKs, generally used to compare pairs of gene sequences, reverse translate and prepare input files. |
| 16 | NG_KaKs_Cal * | 0 | We calculate kaks using bioperl based on the NEi-Gojobori (NG86) algorithm. |
| 17 | Paleo-gene_identifer * | 1 | Self-developed Correspondence process to generate the final mc result file. |
| 18 | Collinearity generator * | 1 | Self-developed to generate a collinear list according to multiple mc results generated. |
| 19 | Paleo-gene_RI * | 0 | Self-developed paleo-gene retention statistical tool based on mc results. |
| 20 | Paleo-gene_RII * | 0 | Self-developed ancient gene loss statistical tool based on mc results. |
| 21 | P-index-calculator * | 1 | Self-developed P-index calculation with customizable parameters. |
| 22 | Draw_list_trees * | 1 | Self-developed tree formation based on collinear list. |
| 23 | GC-calculation * | 0 | Calculation of GC content of genome or CDS sequence. |
| 24 | Chromosome length extractor * | 0 | Chromosome length or gene length statistics. |
| 25 | Gene_cds_exon_counter * | 0 | Calculates the length and proportion of cds, exon, intron, and gene in the original gff file. |
| 26 | Genome Mount Rate Calculator * | 1 | Genome mount rate calculator. |
| 27 | GF_Circos * | 0 | Self-developed ks circle diagram function. |
| 28 | Codonw | 0 | Call Codonw, statistical sequence codon situation. |
| 29 | Cpgfinder | 0 | Call Cpgfinder to find CpG islands in the sequence. |
| 30 | MEME Suite | 0 | Motif of invoked memes, predicted proteins. |
| 31 | GSDS | 0 | Called GSDS to achieve the function of drawing gene structure (CDS, UTR, Intron). |
| 32 | Hmmer | 0 | Invoking the Hmmer for gene family screening. |
| 33 | Pfam | 0 | Pfam is invoked to realize the function of identifying protein domains. |
| 34 | Interproscan | 0 | Invoke interproscan software to achieve gene function annotation. |
| 35 | Seq alignment | 0 | Multi-sequence alignment software (mafft, clustalw, and muscle). |
| 36 | FastTree | 0 | Call FastTree software to achieve the function of building a phylogenetic tree. |
| 37 | IQ-Tree | 0 | Call IQ-Tree software to achieve the function of building a phylogenetic tree. |
| 38 | TransFam identifier | 0 | Regulatory protein (RKs) prediction, invoked by iTak software. |
| 39 | Heatmap * | 1 | Calculate correlations between gene expression patterns and metabolite content patterns and draw heat maps. |
| 40 | Lollipop * | 0 | Draw a lollipop chart function for metabolites or gene expression. |
| 41 | Gene structure * | 0 | Function to visualize the position of genes on chromosomes. |
| 42 | ShinyCircos | 0 | Call ShinyCircos to draw a circos diagram. |
| 43 | Species classification * | 0 | Obtain the classification of the species from NCBI in batches. |
| 44 | SS-extractor * | 1 | Extract gene ID information from pep/cds/gff files based on an ID file. |
| 45 | SAF-converter * | 0 | Format conversions including genbank, fasta, embl, fastq, clustal, phylip, and nexus. |
| 46 | BDI-finder * | 1 | Search and replace tool for file contents. |
| 47 | BDI-deduplicator * | 0 | Delete duplicate gene IDs and sequences in pep or cds files. |
| 48 | BDI-extractor * | 0 | Extract data by column from uploaded files. |
| 49 | BDI-combiner * | 0 | File merge tool for multiple files of the same format. |
| 50 | Deal_stars * | 0 | Delete stop codons ("." and "*") from pep protein files. |
| 51 | Subtree_extractor * | 0 | Extracts a specified range of small phylogenetic trees from a large tree file. |
| 52 | Block_run | 0 | Syntenic analysis tool based on WGDI. |
| 53 | KaKs calculate | 0 | Calculation KaKs tool based on WGDI (Nei-Gojobori algorithm/YN00). |
| 54 | Blast dotplot | 1 | WGDI-based blast dotplot tool. |
| 55 | Ks dotplot | 1 | Ks dotplot tool based on WGDI. |
| 56 | Block_info | 0 | Screening out collinear fragments based on WGDI. |
| 57 | Correspondence | 0 | Correspondence process based on WGDI. |
| 58 | JBrowse | 1 | Gene browser function to view genome and GFF files. |
| 59 | bbm_extraction | 0 | Calculation Tool: BLAST Best Match Extractor. |
| 60 | ks_distriplot | 1 | Visualizing Ks Distributions with Seaborn Ridge Plots. |
| 61 | cds2geno_dotplot | 0 | Synteny Visualization based on CDS Mapping. |
| 62 | mga_circos | 0 | Multi-Genome Analysis: Synteny Visualization. |