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AGRP

Asteraceae Genomic Research Platform

Gene Search

Example:
Example:

All Web-Based Tools

🔥 Top 10 most-used tools are highlighted and shown first. Click Tool Name to sort alphabetically.

No. Tool Name ↕ Usage Count ↓ Description
1 Blast🔥 328 Call the blast software to perform sequence alignment to arbitrary files.
2 Sequence fetch *🔥 92 Find cds and pep sequences for gene ids.
3 Seq alignment🔥 88 Multi-sequence alignment software (mafft, clustalw, and muscle).
4 Sequenceserver🔥 83 Leguminosae sequence alignment and Matching visualization.
5 Diamond🔥 76 Call the Diamond software for sequence alignment, arbitrary files.
6 B_Dotter *🔥 74 Self-developed blastp dot plot function.
7 MCScanX🔥 69 Calls MCScanX software to perform collinearity analysis on arbitrary files.
8 JBrowse🔥 66 Gene browser function to view genome and GFF files.
9 BB_Dotter *🔥 59 Self-developed function of drawing block dot plots.
10 Heatmap *🔥 58 Calculate correlations between gene expression patterns and metabolite content patterns and draw heat maps.
11 Blast match * 44 Leguminosae sequence alignment and best match.
12 ColinearScan 48 Calls the ColinearScan software to perform collinearity analysis on any file.
13 Syntenic visualization 53 A collinear visualization implemented by the invoked Synvisio software based on the results of MCScanX.
14 Dupgen finder 45 The Dupgen finder software is invoked to analyze the type of gene replication.
15 Block number count * 22 Generates the block statistics result based on the ColinearScan result file.
16 ParaAT 36 Call ParaAT to calculate KaKs, generally used to compare pairs of gene sequences, reverse translate and prepare input files.
17 KaKs_Calculator 52 Call KaKs Calculator to calculate KaKs, integrating a variety of algorithms (NG86, YN00, MYN, LWL85, etc.).
18 NG_KaKs_Cal * 25 We calculate kaks using bioperl based on the NEi-Gojobori (NG86) algorithm.
19 BBK_Dotter * 55 Self-developed ks dot plot function.
20 Paleo-gene_identifer * 14 Self-developed Correspondence process to generate the final mc result file.
21 Collinearity generator * 19 Self-developed to generate a collinear list according to multiple mc results generated.
22 Paleo-gene_RI * 16 Self-developed paleo-gene retention statistical tool based on mc results.
23 Paleo-gene_RII * 11 Self-developed ancient gene loss statistical tool based on mc results.
24 P-index-calculator * 12 Self-developed P-index calculation with customizable parameters.
25 Draw_list_trees * 15 Self-developed tree formation based on collinear list.
26 GC-calculation * 37 Calculation of GC content of genome or CDS sequence.
27 Chromosome length extractor * 35 Chromosome length or gene length statistics.
28 Gene_cds_exon_counter * 24 Calculates the length and proportion of cds, exon, intron, and gene in the original gff file.
29 Genome Mount Rate Calculator * 17 Genome mount rate calculator.
30 GF_Circos * 21 Self-developed ks circle diagram function.
31 Codonw 28 Call Codonw, statistical sequence codon situation.
32 Cpgfinder 16 Call Cpgfinder to find CpG islands in the sequence.
33 MEME Suite 54 Motif of invoked memes, predicted proteins.
34 GSDS 38 Called GSDS to achieve the function of drawing gene structure (CDS, UTR, Intron).
35 Hmmer 48 Invoking the Hmmer for gene family screening.
36 Pfam 50 Pfam is invoked to realize the function of identifying protein domains.
37 Interproscan 46 Invoke interproscan software to achieve gene function annotation.
38 FastTree 39 Call FastTree software to achieve the function of building a phylogenetic tree.
39 IQ-Tree 51 Call IQ-Tree software to achieve the function of building a phylogenetic tree.
40 TransFam identifier 19 Regulatory protein (RKs) prediction, invoked by iTak software.
41 Lollipop * 18 Draw a lollipop chart function for metabolites or gene expression.
42 Gene structure * 40 Function to visualize the position of genes on chromosomes.
43 ShinyCircos 33 Call ShinyCircos to draw a circos diagram.
44 Species classification * 21 Obtain the classification of the species from NCBI in batches.
45 SS-extractor * 34 Extract gene ID information from pep/cds/gff files based on an ID file.
46 SAF-converter * 29 Format conversions including genbank, fasta, embl, fastq, clustal, phylip, and nexus.
47 BDI-finder * 23 Search and replace tool for file contents.
48 BDI-deduplicator * 20 Delete duplicate gene IDs and sequences in pep or cds files.
49 BDI-extractor * 22 Extract data by column from uploaded files.
50 BDI-combiner * 18 File merge tool for multiple files of the same format.
51 Deal_stars * 13 Delete stop codons ("." and "*") from pep protein files.
52 Subtree_extractor * 12 Extracts a specified range of small phylogenetic trees from a large tree file.
53 Block_run 14 Syntenic analysis tool based on WGDI.
54 KaKs calculate 23 Calculation KaKs tool based on WGDI (Nei-Gojobori algorithm/YN00).
55 Blast dotplot 27 WGDI-based blast dotplot tool.
56 Ks dotplot 31 Ks dotplot tool based on WGDI.
57 Block_info 13 Screening out collinear fragments based on WGDI.
58 Correspondence 9 Correspondence process based on WGDI.
59 bbm_extraction 18 Calculation Tool: BLAST Best Match Extractor.
60 ks_distriplot 28 Visualizing Ks Distributions with Seaborn Ridge Plots.
61 cds2geno_dotplot 15 Synteny Visualization based on CDS Mapping.
62 mga_circos 20 Multi-Genome Analysis: Synteny Visualization.