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Tools
File Manager
Upload File
from your computer
Text2file
copy the content in the text area to file
Merge
files into one
tar
add files to archive
untar
extract files from archive
Meta Sequence Analyzer
FastaQContig
make contigs using forward and reverse fastaq sequences
Assign Seqs into samples(Updated and slightly tolerant to more errors by beginners)
assign Seqs into Sampels based on primer and barcode sequences.
RetriveDominantSeqbyLength
retrieve majority of sequences accoring to length distribution.
SeqLenDistri
check the length distribution of a fasta seq.
CheckBarcode
If something is wrong with Assign seqs into samples,this tool helps check the barcode pair. you can compare this result and adjust your tag file.
DenoiseAmplicon
remove amplicon or chimera artifacts
Taxonomic OTU reporter
generating TOR based on fasta sequences(No barcode and primer regions,proper names:Sample_(one letter for replicate)numbers e.g. Org_a1179.
UCTaxa2OTUreporter
construct taxonomic OTU reporter using ucfile and taxa assignment
Functional Gene
analysis pipeline for HTS of functional genes.
Uniseqs
get unique seqs from a fasta file.
Seq2OTU
generating an OTU table according to Sequence identity.
BLASTXFrame
get the correct translation frame.
vsearch_derep
remove replicated sequences
vsearch_chimera
remove chimera sequences from the fasta either by denovo or by references
vsearch_cluster
cluster DNA sequences into different groups based on similarity.
vsearch_search
find similar sequences from a database fasta file.
BLASTClassifier
using lowest common ancestor based on blastp/blastn analysis
Core microbiome
from a taxonomic OTUreporter
SeqClusterByDistance
number of clusters under different sequence distance.
CheckSequences
of a fasta file
Count_sample_seqs
of a fasta file
CountFrameShift
based on blastx analysis
SampleGC
calculate the GC content of sample.
Meta Data Manager
Check data frame
:data frame with different number of elements cause problems in the following analysis. Here we kick off those problematic lines.
Select Taxonomic
groups from the data frame
Delete/select Columns
From a data frame.
ListSamples
in a data frame
Rename samples
in a data frame
GetOneWayExperimentDesign
Based on Sample names and Defined levels of Factors.
Select samples
based on sample list,factors,regex and readnums from data frame
Dominat Taxa
which is present in the current taxonomic OTU report
Select Fasta sequences
from a file
Remove Fasta sequences
from a file
Remove Rare OTU
From an OTU reporter
Select_Frequent_OTU
from a taxonomic OTU reporter
Sort_Samples
of a dataframes according treatments or all samples
Combine_colSums
of several dataframes into a new datasets
Combine_Columns
of data frame
TaxaLists
of data frame
AssignBarcode
transform 2D dataframe to Arrays(mxd format)
Meta Diversity Analyzer
Count taxnomic numbers
based on a a taxnomic otu reporter
AutoSample
group samples based on their characteristics(sep by ",".
Basic_Summary
of a taxonomic OTU reporters
Sum up Tax
from the data frame
Calculate bray curtis
based on a data frame
Variation of community composition within treatments
based on pairwised distances.
Boxplot(ggplot)
of dataframes
Module_Summary
based on an taxonomic OTUreporter and modules
UPGMA cluster
analysis based on a dist matrix
Permutation test
to analyze significant difference between community composition based on a pairwise distance matrix
Permutation test
based on a hybridized distance matrix or similarity matrix.
ANOSIM
of a taxonomic OTU reporter to analyze significant difference between treatments;基于OTUreporter或距离矩阵分析不同组之间的差异
Alpha Diversity
of each sample
Relative/Absolute abundance
of a data frame
Barplot
of mean+sd tables.
Paired barplot
of two data frame or one data frame
One Way Multicomp
using glm model for binary data(negative binomial test.)
Combine tables
into a result table.
Compare_treatments
dissimilarity between treatments based on a dist matrix
Statistic image
mark statistic result in a manner of heatmap style.
One_Way_Multicomp3
using TukeyHSD or negative binomical tests
DFPostHSDPvals
calculated pairwise p-values using different posthoc tests.
MultiwayANOVA
make multiple ANOVA for a dataframe.
Heatmap
analysis of selected taxa(species)
BLAST
analyses locally
NMMD
based on a dist matrix
PCoA
based on a dist matrix
RDA
analyses and plot
RDA/CCA/NMMD
analyses and plot
Mantel tests
不同环境变量对种群结构的解释能力.
PCA
analyses and plot
PLSDA
analyses and plot
SpearmanNet
for analyze microbial network
IndicativeNetwork
indicates association of taxa with one or the other treatments.
Correlations
between Taxonomic OTU reporter and Environmental variables.
Kmer Cluster
analyses and plot
Variation_Partion
of community composition using different sets of explaining matrixs
Boxplot
of community composition using different sets of explaining matrixs
Rarefaction
analysis of a taxonomic OTU reporters
Plot_Rare_lines
of a rarefaction table
LibCompareTab
statistic analysis usng the algorithm describled in RDP libcompare.
RespondingBox/Barplot
identify association between responses and envparaments
Pieplot
of dataframe.
Statistic2BiNetwork
construct a network based on statistic analysis
Mantel
tests between two distant matrix or dataframe.
RandomForest
to identify key tax discrimnative among treatments.
CompareOTUreporter
compare common samples in two OTUreporter.
CountRelativeAbundance
Count the number of taxa with a minimum relative abundace.
Correlation Plot
based on a dataframe
Composite tools
RespondingPairedBar
Based on statistic tables
Image
for plotting an image based on a dataframe.
Pairwise Mantel
tests among distance matrix or dataframe.
Metagenomic Tools collected
Normalize by Copy Number
Predict Metagenome
Categorize by Function
Metagenome Contributions
Tentative AI Analyzer
OneWayOptimizationPCA
analyses and plot
Plots
based on data frames.
SEM
analysis to relationship between datasets.
GetDataFromPublicDB
Connect to Genbank
Get Microbial Data
Download_Seq_From_NCBI
based on an file with all accession numbers.
Transcriptomics
SeqsintoGroups
based on sequence identity
RetriveSeqViaAcc
Download Gene/genomic sequences from GenBank via accession numbers
Genome2genes
Parse a genbank format genome sequences into genes and ammino seqs.
Multiple BLASTN
analyses agains a database
RNA Mapping
summary based on BLASTN reporter
Table
generator based on mapped
Annotation
genes based on blastp analysis
BLASTP2KO2GO
based on ammino acid sequences of genes
De Nova
assembler of RNA-seq.
SOAPDenovo
assembler of RNA-seq.
tRNAscanSE
searching for tRNA genes in genomic(DNA) sequences.
Transdecoder
of transcripts of RNA-seq.
ORFfinder
(open reading frame) finder using fasta sequences
Mapping
short sequences against a database using BWA or Magic Blast
HTSeq Coverage
calculator of sam files
RPKM
of HTS dataframe
Pathway/GeneSets
expression based RPKM of genesets.
Pathway/Genesets
enrichment analysis using Gesa.
GeneNetwork
by distance or correlations.
Gene2Pathway
summary gene list to pathway.
Spider Clouds
plot dots according to their affinity to treatments.(gc_ding).
TranOpenron
Retrieve operon using draft genome and transcriptomics.
Genome
RAPT
assemble and annotation of genomes.
PGAP
genomes annotation using NCBI PGAP pipeline.
AntiSMASH
预测抗生素/抗菌肽合成基因簇.
KOFamScan
基于KEGG的kofamscan注释基因(氨基酸序列）。Annotating AA sequences to KEGG KO using kofamscan.
SelectTopKOs
筛选最相近KO,Select the toppest KO.
Gene prediction
using glimmer3
Gene validation
based on blastp and hmm analysis.
Gene prediction
using GeneMarkSuites
Genome plot
using genoPlotR
Gene2COG
Gene annotation to cog using blastp
Gene2Pathway
summary gene list to pathway.
Pathway/Module2genes
gene list of pathway.
Add_Colors
of a fasta sequence
Combine_Annotation
of a genome
Add_annotation
of a fasta sequence
PyCoreGenome
calculate pearson and spearman correlation for a dataframe.
KEGG tools
Display
database release and linked database informations KEGG(www.kegg.jp)
Obtain
a list of entries identifier and associated defination from KEGG(www.kegg.jp)
Retrieve
given database entries from KEGG(www.kegg.jp)
Find
relatied entries by using database cross-reference in KEGG(www.kegg.jp)
Find
entries with matching query keyword or other query data from KEGG(www.kegg.jp)
Convert
KEGG identifier to outside identifier or vice versa
Find
adverse drug-drug interactions from KEGG(www.kegg.jp)
Retrive
all genes of a KEGG organisms(www.kegg.jp)
List
genes in pathway of a KEGG organisms(www.kegg.jp)
Tentative Literature Analyzer
Retrieve Key Sentences
from a paper or web page.(So far, Only english)
Para2sents
split paragraph into sentences(text)
Get Sentences
from Sentences lines with words/phase
WordFreq
analyses of inputed text
Get Similar sentences
from a data bases(ghostwriter----based on ChenChenMatrix)
PDF2TEXT
Transformation PDF into Text.
Format Article
Format an article for DB construction
Load Article
into database(Only for developping team)
Load Sentence
into database(Only for developping team)
Load Abstract
into database(Only for developping team)
Query Article DB
for sentences with keywords.
Parse Article
Parse articles using python
Science Parser
parse Science paper into json format.
Abao's research
vennplot
for different samples(max 5)
Heatmap2
analysis
Download
Sequences from uniport based on uniport id.
Enrichment
analysis of pathway,genesets or taxonomic group
HorizBarplot
of pathway enrichemnt analysis.
Rhizosphere
RootCalibration
calculate pairwise distance between sampling points.
AssignSamp2Roots
assign samples to its coordination according to log and samle name.
HistPairWiseDistance
describle the distribution of pairwise distance.
RenameRootPoints
rename root point.
RenameDistMatrix
rename the distance matrix according to sampcood2sampname.
CommunityToSpatial
diffence in community composition vs difference in spatial distance.
PyCorrelation
calculate pearson and spearman correlation for a dataframe.
CoOcurringNetWork
基于最小相对丰度，发现共存类群，构建共现网络.
Radfit
analysis of a taxonomic otu reporter.
Miscellaneous tools
RDP classifier(2.01)
of sequences data
Qiime2RDP
Qiime classifier to RDP classifier
Community compositon comparison
between different methods using pairwise braycurtis distance.
Spider Plot
of data according to known factors.
Generating
Barcode primers
Map Seqs
between database
Remove OTUs
of a complex inoculant
Make Table
based on denove OTU picking
AlignTable
OTU report according to sequence numbers
FormatPathogenReporter
split the subspecies column into species .
Select
unique seqs by ids
Parse
Blast reporter
Split Fastq
into samples
Gene(translation)
to amino acid seqs.
Select
seqs by length
Representative seqs
of a set of fasta sequences
Data distribution
analysis using PDFs of normal,lognormal,logistic and gamma.
Data transformation
using log, byrow and bycol.
PyDatatransform
transform dataset using python3 packages.
BLAST
analysis (Standalone) .
Genome2Genes
for genome plots.
Run
linux command
Genbank2Fasta
convert genbank format into fasta format
2Dto1D
Transform 2D tables into 1D array(Tables seperted by \n\n)
1Dto2D
Transform 1D tables into 2D array(Tables seperted by \n\n)
MarkinChina
Mark your sample points in the map of China
NMMD
based on a dataframe
SpearmanNet2
construct network without data transformation.
StatisticNet
generate an network based on statistic analysis
AlignColums
align 2 tables into 1 tables according to key
DownLoadSeqFromNCBI
using id files
Rename seq
of a fasta in batch mode
Rename seq2
Multiple Sequences
Rename Fasta
by sequence description
Select_OTUs
with the highest abundant from samples
Select_OTUs
from a taxonomic OTU reporter with minimum number of reads
2DtoArrays
transform 2D dataframe to Arrays(mxd format)
UC2list
convert a uc(10 columns)into 2column lists
List2Table
convert a 2column lists into 2D table
Plot_Distmatrix
plot a distance matrix.
Plot_image
plot images of a dataframe
Count_Sig_table
from a combined statistic table
Combine_Multi_Table
based on the first columns.
MapBacterialPathogens
detect potential bacterial pathogens 16S rRNA sequences.
BiDataframeCompare
compare two dataframe.
Retrieve_Seqs
based on sample names.
CombineDifferntTablesBySamples
Combine multiple tables into a dataframe according to sample names(Only consider samples in all tables).
Assign the taxa
into its parent's taxrank using NCBITAX.
Add_Tag
to a dataframe
Select_module
transform 2D dataframe to Arrays(mxd format)
AddTaxa2Seq
based on the classification
Paired Correlation
between two dataframe
Fasta2Fasta
retrieve fasta seqs from the reference using the ids from the other fasta.
SelectRespondingTaxa
from a statistic analysis.
Geneid2Description
assign gene description to data frame.
FastqCounter
counts read number in fastq libraries.
SelectSubgraphbyNode
from a gml format network.
Multipatt
of a data frame
GetRange
get the ranges for the dataframe
BraydistBoxplot
of a distant matrix
rgbcolor2hex
change rgb color into hex color format.
NetworkComparisons
calculate the distance between networks
BaTS
calculate significance between treatments based on phylogenetic relationships
ImageSplitDf
split the statistic table for the image plot.
RenameTarfile
rename files in a tar folders.
2aliyun
send files to aliyun server
generalspecialist
分析种群结构特征.
speciesdistribution
分析物种分布特征.
CombinePDF
two pdfs page by page.
SelectTopNByTaxa
select top n OTUs with highest abundance.
SelectColumn
select the columns with the value .
Sequence Analysis
Make_Contig
using pairwise alignment(We trust the begining of forward or reverse sequences).
MultipleAlignment
of DNA or AA seqs
CheckAlignment
remove undesired region of a multiple sequence alignment.
Adjust_Oritention
of DNA sequences
Denoise_16S_rRNA
of a fasta query file
Get_16S_rRNA
reference sequecnes of a fasta query file
SelectSeqsByName
从数据库中筛选出需要的序列.
Alignment_of_16S
rRNA genes using mothur
Select_seqs_by_id
from a fasta file
Classifier
of 16S rRNA or other functional gene sequences.
Overlapped_seqs
between bidirectional sequences
AlignQual
measurement of quality of bidirectional sequences based on multiple alignments.
Get_Seqs
by ids.
Count_seqs
in file(fasta/fastq).
CountSilvaSpecies
of species in a given genus in silva database.
RetrieveSilvaRep
retrieve representative speices sequences selected from the silva database.
CalSpeciesDist
similarity within species and between species in silva database.
Fastq2fasta
convert a fastq format file into fasta
Subseq of fasta
retrieve subseqs from a fasta files
Translate
DNA sequences into AA.
Calculate_Pairwise
distance between DNA sequences.
GetWithinDist
using pairwise distance and seq2otu assignment.
Retrieve Sequences
from a blast databases..
ModiFastaId
modified the id of fasta file..
RetriveNCBIRefbyBlastn
from the reference genomes(NCBIRef).
NCBIRef16SrRNA
retrieve corresponding 16S rRNA gene from NCBIrefgenome.
FastTree
construct phylogenetic tree based on aligned DNA or AA sequences.
LibCompare
statistic analysis for library comparison.
ePCR
analysis of batch sequence data
Gene2Gene
is analysis to find out genes presented in common geneme(NCBIRef).
blastx
analysis against bacteriaref curated from NCBI
CommonForRev
for short reads analysis(Get common sequneces based on id or description from paired reads.
RandomSamplingSeqs
retrieve randomly from the fasta files
DecorateTree
assign background color to a tree.
CommonFastq
retrieve common sequence from paired fastq files based on seqid.
RetrieveSeqwithSite
提取具有特定位点的DNA序列.
Endonuclease
DNA内切酶分析.
Meta_Analyzer2
FastqChecker
check the rawdata of fastq files.
FastqFilter
Filter low quality sequences in a fastq library.
Retrieve16S/18S
rRNA gene from metagenomic library.
Kraken
classify sequences into taxa
Diamond
a blastx/n programe to analyze large datsets.
Megahit
make contig with megahits.
PRODIGAL
predict prokaryotic genes
Coocurrence Network
based on OTU reporter.
NetCoverage
calculate the coverage of modules in different samples
SPAdes
assemble contigs with the packages of SPAdes verion 3.14
MetaGeneMarkerS
predict gene using the metagenomic models
KO2Modules
map KEGG module based on KOs
MetaCompVenn
map KEGG module based on KOs
RespondingJaccard
calculate responding patterns
EsGecopyPerBillion
estimate gene copy numbers in per billion reads.
LibCompareFolds
statistic analysis usng the algorithm describled in RDP libcompare.
RetrieveSeq
with high similarity to the provided reference from a metagenomic library .
MetaModuleSummary
make a summary of module according to the gene and taxa
CheckKEGGModuleBritebyTaxa
Check summarized KEGG module/brite by Taxa. 根际不同KEGG moudle 和Brite的分析结果。
PyDataManager
modify dataframe using python3 packages. 利用Pandas包操作数据框。
CountRatio
calculate the log2 of ratio of counts seperated by the taxrank and value.
RankedStack
plot the number of responding genes according to responding level and taxa.
RhizosphereRatio
Diversity or population.
KEGGMapGeneAbundance
calculate the geneabundance for KEGG pathways(Shotgun metagnomics).
DifferenntKEGGmapsbetweenTreatments
map the pathways based on mapped.
RetrieveMap
from data from the mapping .
MappingKEGGbyKOs
color the KEGG pathway by KOs.
Tool Design
LAMPDesign
根据序列文件(fasta格式)设计LAMP引物.
ReactorController
CompostReactor
堆肥反应控制单元.
Incubator
菌体发酵控制器.
LEfSe
Taxaotureporter2LeFse
split the subspecies column into species .
A) Format Data for LEfSe
B) LDA Effect Size (LEfSe)
C) Plot LEfSe Results
D) Plot Cladogram
E) Plot One Feature
F) Plot Differential Features
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