263 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset 3
Align reads and estimate abundance on a de novo assembly of RNA-Seq data 11
alimask append modelmask line to a multiple sequence alignments 5
AnnotateBed annotate coverage of features from multiple files 17
AXT to concatenated FASTA Converts an AXT formatted file to a concatenated FASTA alignment Conversion 1
AXT to FASTA Converts an AXT formatted file to FASTA format Conversion 1
AXT to LAV Converts an AXT formatted file to LAV format Conversion 1
BAM to BED converter 21
BAM to fastq Convert BAM file to fastq 1
Bar chart for multiple columns 1
Barcode Splitter 6
BED to BAM converter 18
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 17
BEDPE to BAM converter 18
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
Bowtie2 - map reads against reference genome 22
Boxplot of quality statistics 2
Build expression matrix for a de novo assembly of RNA-Seq data by Trinity 11
CD-HIT PROTEIN Cluster a protein dataset into representative sequences 4
CD-HIT-EST Cluster a nucleotide dataset into representative sequences 3
Change Case of selected columns 1
Clip adapter sequences 5
ClosestBed find the closest, potentially non-overlapping interval 17
ClusterBed cluster overlapping/nearby intervals 17
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
Collapse sequences 4
Column Regex Find And Replace 3
Compare two Datasets to find common or distinct rows 1
ComplementBed Extract intervals not represented by an interval file 18
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 18
Compute quality statistics 4
Concatenate datasets tail-to-head 1
Convert delimiters to TAB 1
Convert BCF to BCF_BGZIP 1
Convert BCF_BGZIP to BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert FASTA to 2bit 2
Convert FASTA to Bowtie base space Index 1
Convert FASTA to Bowtie color space Index 1
Convert FASTA to len file 1
Convert FASTA to Tabular 1
Convert from BAM to FastQ 14
Convert Genomic Intervals To BED 1
Convert Genomic Intervals To Coverage 2
Convert Genomic Intervals To Strict BED 1
Convert Genomic Intervals To Strict BED12 1
Convert Genomic Intervals To Strict BED6 1
Convert GFF to BED 1
Convert GFF to Feature Location Index 1
Convert Len file to Linecount 1
Convert lped to fped 1
Convert lped to plink pbed 1
Convert MAF to Fasta 1
Convert MAF to Genomic Intervals 1
Convert Picard Interval List to BED6 converter 1
Convert plink pbed to ld reduced format 1
Convert plink pbed to linkage lped 1
Convert SAM to BAM 1
Convert tabular to dbnsfp 1
Count occurrences of each record 2
Create single interval as a new dataset 1
Cuffcompare compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments 14
Cuffdiff find significant changes in transcript expression, splicing, and promoter use 13
Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data 11
Cuffmerge merge together several Cufflinks assemblies 12
Cuffnorm Create normalized expression levels 5
cummeRbund visualize Cuffdiff output 3
Cut columns from a table 2
Differential expression analysis using a Trinity assembly 11
Draw nucleotides distribution chart 4
Draw quality score boxplot 5
ExpandBed replicate lines based on lists of values in columns 17
Extract features from GFF data 1
Extract Genomic DNA using coordinates from assembled/unassembled genomes 7
Extract MAF blocks given a set of genomic intervals 1
Extract MAF by block number given a set of block numbers and a MAF file 1
Extract Pairwise MAF blocks given a set of genomic intervals 1
FASTA from text Simple creation of FASTA file from text area field. 1
FASTA Width formatter 4
FASTQ Groomer convert between various FASTQ quality formats 4
FASTQ to FASTA converter from FASTX-toolkit Sequence conversion 5
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 17
FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data 1
Faux Interproscan Interproscan functional predictions of ORFs (faux). Input file and computation options are ignored (other than the types of outputs). The same precomputed results are produced every time. 1
Fetch closest non-overlapping feature for every interval Filtering 4
Filter data on any column using simple expressions Formatting 1
Filter by quality 5
Filter GFF data by attribute using simple expressions 3
Filter GFF data by feature count using simple expressions 2
Filter GTF data by attribute values_list 1
Filter low expression transcripts from a Trinity assembly 11
Filter MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
FisherBed calculate Fisher statistic between two feature files 17
FlankBed create new intervals from the flanks of existing intervals 18
Gene BED To Exon/Intron/Codon BED expander 1
Generate gene to transcript map for Trinity assembly 11
Genome Coverage compute the coverage over an entire genome 18
Get Microbial Data 1
GetFastaBed use intervals to extract sequences from a FASTA file 17
GFF-to-BED converter Conversion 1
Group data by a column and perform aggregate operation on other columns. 3
GroupByBed group by common cols and summarize other cols 17
GTF-to-BEDGraph converter Conversion 1
hmmalign align sequences to a profile HMM 5
hmmbuild Build a profile HMM from an input multiple alignment 5
hmmconvert convert profile file to a HMMER format 5
hmmemit sample sequence(s) from a profile HMM 5
hmmfetch retrieve profile HMM(s) from a file 5
hmmscan search sequence(s) against a profile database 5
hmmsearch search profile(s) against a sequence database 5
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
Interproscan Interproscan functional predictions of ORFs. 1
Intersect the intervals of two datasets Filtering 7
Intersect intervals find overlapping intervals in various ways 17
JaccardBed calculate the distribution of relative distances between two files 17
jackhmmer iteratively search a protein sequence against a protein database (PSIBLAST-like) 5
Join the intervals of two datasets side-by-side Aggregation 5
Join MAF blocks by Species 1
Join two Datasets side by side on a specified field 3
LAV to BED Converts a LAV formatted file to BED format 1
Length Distribution chart 3
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 17
MAF Coverage Stats Alignment coverage information 1
MAF to BED Converts a MAF formatted file to the BED format 1
MAF to FASTA Converts a MAF formatted file to FASTA format 1
MAF to Interval Converts a MAF formatted file to the Interval format 1
MakeWindowsBed make interval windows across a genome 18
Map small RNA Against miRBase repository 1
Map with BWA - map short reads (< 100 bp) against reference genome 15
Map with BWA-MEM - map medium and long reads (> 100 bp) against reference genome DNA mapping Genetic mapping Genome annotation Mapping Mapping assembly Protein SNP mapping Sequence assembly Sequence tag mapping 17
MapBed apply a function to a column for each overlapping interval 17
MaskFastaBed use intervals to mask sequences from a FASTA file 17
Merge the overlapping intervals of a dataset Sequence merging 5
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 17
Merge Columns together 2
MergeBED combine overlapping/nearby intervals into a single interval 17
MIRA v4.0 de novo assember Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads 1
MIRA v4.0 mapping Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads 1
MIRA v4.0 mirabait Filter reads using kmer matches 1
miRanda finds potential target sites for miRNAs in genomic sequences 2
MiRDeep2 identification of novel and known miRNAs 3
MiRDeep2 Mapper process and map reads to a reference genome 4
MiRDeep2 Quantifier fast quantitation of reads mapping to known miRBase precursors 2
MOL to CML 2
MOL to MOL2 2
MOL to SMILES 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
MOL2 to SMILES 2
MultiCovBed counts coverage from multiple BAMs at specific intervals 17
Multiple Intersect identifies common intervals among multiple interval files 21
NCBI BLAST+ blastdbcmd entry(s) Extract sequence(s) from BLAST database Data retrieval Database search 16
NCBI BLAST+ blastn Search nucleotide database with nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastp Search protein database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ blastx Search protein database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 16
NCBI BLAST+ convert2blastmask Convert masking information in lower-case masked FASTA input to file formats suitable for makeblastdb Conversion 12
NCBI BLAST+ database info Show BLAST database information from blastdbcmd Data retrieval 16
NCBI BLAST+ dustmasker masks low complexity regions Sequence complexity calculation 14
NCBI BLAST+ makeblastdb Make BLAST database Genome indexing 17
NCBI BLAST+ makeprofiledb Make profile database Genome indexing 10
NCBI BLAST+ rpsblast Search protein domain database (PSSMs) with protein query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ rpstblastn Search protein domain database (PSSMs) with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 15
NCBI BLAST+ segmasker low-complexity regions in protein sequences Sequence complexity calculation 12
NCBI BLAST+ tblastn Search translated nucleotide database with protein query sequence(s) Data retrieval Database search Sequence similarity search 17
NCBI BLAST+ tblastx Search translated nucleotide database with translated nucleotide query sequence(s) Data retrieval Database search Sequence similarity search 17
nhmmer search a DNA model or alignment against a DNA database (BLASTN-like) 5
nhmmscan search DNA sequence(s) against a DNA profile database 5
NucBed profile the nucleotide content of intervals in a FASTA file 17
OverlapBed computes the amount of overlap from two intervals 17
Paste two files side by side 1
phmmer search a protein sequence against a protein database (BLASTP-like) 5
Quality format converter (ASCII-Numeric) 4
RandomBed generate random intervals in a genome 18
Regex Find And Replace 2
ReldistBed calculate the distribution of relative distances 17
Remove beginning of a file 1
Remove sequencing artifacts 5
Rename sequences 5
RepeatMasker RepeatMasker 4
Reverse Complement a MAF file 1
Reverse-Complement 5
RNA/DNA converter 5
RNA2Dfold explore structure space between two reference structures 1
RNAaliduplex find binding sites of two RNA alignments 1
RNAalifold Calculate minimum free energy secondary structures and partition function on a multiple alignment file 1
RNAcofold Calculate secondary structures of two RNAs with dimerization 1
RNAdistance Calculate distance between secondary structures of two RNAs 1
RNAduplex Compute the structure upon hybridization of two RNA strands 1
RNAeval Calculate energy of RNA sequences with given secondary structure 1
RNAfold Calculate minimum free energy secondary structures and partition function of RNAs 1
RNAheat Calculate energies of RNA in a temperature range 1
RNAinverse Calculate RNA sequence from secondary structure 1
RNALalifold Calculate locally stable secondary structures for a set of aligned RNAs 1
RNALfold calculates locally stable secondary structures of RNA 1
rnammer RNAmmer predicts 5S/8S, 16S/18S, and 23S/28S ribosomal RNA in genome sequences. 1
RNApaln RNA alignment based on sequence base pairing propensities 1
RNApdist Calculate distances between thermodynamic RNA secondary structure ensembles 1
RNAPKplex predicts RNA secondary structures including pseudoknots 1
RNAplex Find targets of a query RNA 1
RNAplfold predicts RNA secondary structures including pseudoknots 1
RNAplot Draw RNA Secondary Structures 1
RNASeq samples quality check for transcript quantification 11
RNAsnoop Find targets of a query H/ACA snoRNA 1
RNAsubopt Calculates suboptimal secondary structures of RNAs 1
RNAup Calculate the thermodynamics of RNA-RNA interactions 1
SDF to CML 2
SDF to InChI 2
SDF to mol2 2
SDF to SMILES 2
Secure Hash / Message Digest on a dataset 1
Select lines that match an expression 1
Select first lines from a dataset 1
Select last lines from a dataset 1
Select random lines from a file 2
SFF converter 1
ShuffleBed randomly redistrubute intervals in a genome 18
SlopBed adjust the size of intervals 18
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
Sort data in ascending or descending order 2
SortBED order the intervals 17
SpacingBed reports the distances between features 13
Split MAF blocks by Species 1
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
StringTie transcript assembly and quantification 13
StringTie merge transcripts 7
Subtract the intervals of two datasets Filtering 7
SubtractBed remove intervals based on overlaps 17
Summary Statistics for any numerical column 3
Tabular-to-FASTA converts tabular file to FASTA format 2
TagBed tag BAM alignments based on overlaps with interval files 17
TopHat Gapped-read mapper for RNA-seq data 12
TransDecoder Find coding regions within transcripts 4
Trim leading or trailing characters 1
Trim sequences 6
Trimmomatic flexible read trimming tool for Illumina NGS data Sequence trimming 13
Trinity de novo assembly of RNA-Seq data 13
Upload File from your computer 2
VCF to MAF Custom Track for display at UCSC 1
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
Wiggle-to-Interval converter 1
WindowBed find overlapping intervals within a window around an interval 17