Selected Analysis Tools

Number	Tools	Description
1	Blast	Call the blast software to perform sequence alignment to arbitrary files.
2	Diamond	Call the Diamond software for sequence alignment, arbitrary files.
3	*Blast match	Leguminosae sequence alignment and best match.
4	*Sequence fetch	Find cds and pep sequences for gene ids.
5	Sequenceserver	Leguminosae sequence alignment and Matching visualization.
6	MCScanX	Calls MCScanX software to perform collinearity analysis on arbitrary files.
7	ColinearScan	Calls the ColinearScan software to perform collinearity analysis on any file.
8	Syntenic visualization	A collinear visualization implemented by the invoked Synvisio software based on the results of MCScanX.
9	Dupgen finder	The Dupgen finder software is invoked to analyze the type of gene replication.
10	*Block number count	Generates the block statistics result based on the ColinearScan result file.
11	ParaAT	Call ParaAT to calculate KaKs, which is generally used to compare pairs of gene sequences, reverse translate and prepare input files, and then call external software such as KaKs Calculator or PAML to perform the actual Ka/Ks calculation.
12	KaKs_Calculator	Call KaKs Calculator to calculate KaKs, integrating a variety of algorithms (such as NG86, YN00, MYN, LWL85, LPB93, MLWL), providing flexible calculation options.
13	*NG_KaKs_Cal	We calculate kaks using bioperl based on the NEi-Gojobori (NG86) algorithm.
14	*B_Dotter	Self-developed blastp dot plot function.
15	*BB_Dotter	Self-developed function of drawing block dot plots.
16	*BBK_Dotter	Self-developed ks dot plot function.
17	*Paleo-gene_identifer	Self-developed Correspondence process. According to the block diagram pixel file, blast, block, gff, lens file, generate the final mc result file.
18	*Collinearity generator	Self-developed to generate a collinear list according to multiple mc results generated.
19	*Paleo-gene_RI	Self-developed paleo-gene retention statistical tool based on mc results.
20	*Paleo-gene_RII	Self-developed ancient gene loss statistical tool based on mc results.
21	*P-index-calculator	Self-developed P-index calculation, which can be two sets or multiple sets. There are parameters on the page, which can be set by yourself.
22	*Draw_list_trees	Self-developed tree formation based on collinear list.
23	*GC-calculation	Calculation of GC content of genome or CDS sequence.
24	*Chromosome length extractor	Chromosome length or gene length statistics.
25	*Gene_cds_exon_counter	Calculates the length and proportion of cds, exon, intron, and gene in the original gff file.
26	*Genome Mount Rate Calculator	Genome mount rate calculator.
27	*GF_Circos	Self-developed ks circle diagram function.
28	Codonw	Call Codonw, statistical sequence codon situation.
29	Cpgfinder	Call Cpgfinder to find CpG islands in the sequence.
30	MEME Suite	Motif of invoked memes, predicted proteins.
31	GSDS	Called GSDS, to achieve the function of drawing gene structure (CDS, UTR, Intron).
32	Hmmer	Invoking the Hmmer for gene family screening.
33	Pfam	Pfam is invoked to realize the function of identifying protein domains.
34	Interproscan	Invoke interproscan software to achieve gene function annotation.
35	Seq alignment	Three multi-sequence alignment software (mafft, clustalw, and muscle) are called, which is optional.
36	FastTree	Call FastTree software to achieve the function of building a phylogenetic tree.
37	IQ-Tree	Call IQ-Tree software to achieve the function of building a phylogenetic tree.
38	TransFam identifier	Regulatory protein (RKs) prediction, invoked by iTak software, enables predictive transcription factors (TFs), transcription regulatory factors (TRs), and protein kinases (PKs).
39	*Heatmap	The transcriptome and metabolome are combined to calculate Pearson coefficient to see the correlation between gene expression patterns and metabolite content patterns in each tissue, determine the correlation between genes and metabolites, and draw heat maps.
40	*Lollipop	Draw a lollipop chart function. It can be a metabolite or the number of genes that function as expressed.
41	*Gene structure	Function, the position of genes on chromosomes.
42	ShinyCircos	Call ShinyCircos to draw a circos diagram.
43	*Species classification	According to the Latin name of the input species, obtain the classification of the species from NCBI in batches.
44	*SS-extractor	It is a gene sequence extraction tool. Upload pep file, cds file, gff file and ID file, and extract the corresponding gene ID information from the other three files according to the id file.
45	*SAF-converter	Global multi-sequence alignment file format conversion tool (pep or cds file). Format conversions for various file types are available, including genbank, fasta, embl, fastq, clustal, phylip, and nexus.
46	*BDI-finder	Search and replace tool. This is a search and replace tool. You can upload a file and specify which characters to replace and which characters to replace. The tool looks for all matches in the file and replaces them with what you specify.
47	*BDI-deduplicator	In the pep or cds file, delete the duplicate gene id and sequence according to the gene id.
48	*BDI-extractor	This is a tool for extracting data by column. You can upload the file and specify the column number to be extracted, and the tool will extract the data for the corresponding column from the file.
49	*BDI-combiner	File merge tool. Upload multiple files of the same file format and eventually return a combined total file.
50	*Deal_stars	Delete ". "from the pep protein file. And "*". The ". "in the Pep file And "*" stand for stop codons, which will report errors when running some software, such as diamond and interproscan. Cds file is not supposed to appear "." And "*".
51	*Subtree_extractor	From a large phylogenetic tree file (can be a species tree, can be a gene tree), extracts a specified range of small phylogenetic trees.
52	Block_run	Syntenic analysis tool based on WGDI.
53	KaKs calculate	Calculation KaKs tool based on WGDI. The Ka/Ks is calculated using the Nei-Gojobori algorithm in the YN00 program based on PAML software.
54	Blast dotplot	WGDI-based blast dotplot tool.
55	Ks dotplot	Ks dotplot tool based on WGDI.
56	Block_info	Screening out collinear fragments based on WGDI.
57	Correspondence	Correspondence process based on WGDI.
58	JBrowse	Call Jbrowse, to achieve the gene browser function, you can view the genome and GFF and other files.