312 tool(s) found

Tool Description Topics Available version(s)
Add column to an existing dataset 3
Admixture a population structure from large SNP genotype datasets 1
Annotate a VCF dataset with custom filters 2
AnnotateBed annotate coverage of features from multiple files 17
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 4
Association using GLM (General Linear Model) 1
Association using MLM (Mixed Linear Model) 1
backtranseq Back translate a protein sequence 5
BAM to BED converter 21
banana Bending and curvature plot in B-DNA 5
Batch-get-subseq Batch extract sub-sequences from new draft rice genomes 1
bcftools convert to vcf Converts other formats to VCF/BCFk 2
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 9
Beagle Beagle version 4.0 performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection 2
BED to BAM converter 18
BED to IGV create batch script for taking IGV screenshots 10
BED-to-bigBed converter Conversion 2
BED-to-GFF converter Conversion 1
BED12 to BED6 converter 17
BEDPE to BAM converter 18
biosed Replace or delete sequence sections 5
Blat Alignment Filter Stringent filtering of alignment results (psl v3, from blat) 1
Boxplot of quality statistics 2
btwisted Calculates the twisting in a B-DNA sequence 5
cai CAI codon adaptation index 5
cai custom CAI codon adaptation index using custom codon usage file 5
Calculate Distance Matrix from Genotype Data 1
Calculate Kinship from Genotype Data 1
Change Case of selected columns 1
chaos Create a chaos game representation plot for a sequence 5
charge Protein charge plot 4
Check GWAS Inputs checks concordance between input files for GWAS analysis 3
checktrans Reports STOP codons and ORF statistics of a protein 4
chips Codon usage statistics 5
cirdna Draws circular maps of DNA constructs 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
codcmp Codon usage table comparison 5
coderet Extract CDS, mRNA and translations from feature tables 5
Compare multiple VCF datasets 2
Compare two Datasets to find common or distinct rows 1
ComplementBed Extract intervals not represented by an interval file 18
compseq Count composition of dimer/trimer/etc words in a sequence 4
Compute an expression on every row 3
Compute both the depth and breadth of coverage of features in file B on the features in file A (bedtools coverage) 18
compute R2 compute R-squared value of a prediction vs true phenotype 1
Concatenate datasets tail-to-head 1
Concatenate multiple datasets tail-to-head 1
Condense consecutive characters 2
Convert delimiters to TAB 1
Convert BCF to uncompressed BCF 1
Convert BED to Feature Location Index 1
Convert BED to GFF 1
Convert bed/bim/fam to ped/map 1
Convert bim/fam/bed to VCF 1
Convert Biom1 to Biom2 1
Convert Biom2 to Biom1 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 fai file 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 Ref taxonomy to Seq Taxonomy converts 2 or 3 column sequence taxonomy file to a 2 column mothur taxonomy_outline format 1
Convert SAM to BAM 1
Convert tabular to dbnsfp 1
Convert uncompressed BCF to BCF 1
Count occurrences of each record 2
cpgplot Plot CpG rich areas 5
cpgreport Reports all CpG rich regions 4
Create single interval as a new dataset 1
cusp Create a codon usage table 5
Cut columns from a table 2
cutseq Removes a specified section from a sequence 4
Cytoscape Visualize interaction networks from JSON file 2
dan Calculates DNA RNA/DNA melting temperature 4
Decompress an archive in zip, gz, tar.gz, fastq.gz, fastq.bz2 or tar.bz2 format 3
degapseq Removes gap characters from sequences 5
descseq Alter the name or description of a sequence 5
diffseq Find differences between nearly identical sequences 4
digest Protein proteolytic enzyme or reagent cleavage digest 5
Diversity by gene calculates various diversity indexes with EggLib. 2
dotmatcher Displays a thresholded dotplot of two sequences 4
dotpath Non-overlapping wordmatch dotplot of two sequences 4
dottup Displays a wordmatch dotplot of two sequences 4
dreg Regular expression search of a nucleotide sequence 5
einverted Finds DNA inverted repeats 4
encode encode genotypes for further machine learning analysis 1
epestfind Finds PEST motifs as potential proteolytic cleavage sites 4
equicktandem Finds tandem repeats 4
est2genome Align EST and genomic DNA sequences 4
etandem Looks for tandem repeats in a nucleotide sequence 4
evaluation evaluate results of classifiers prediction 1
ExpandBed replicate lines based on lists of values in columns 17
Extract features from GFF data 1
extractfeat Extract features from a sequence 4
extractseq Extract regions from a sequence 5
Fastme Calculate distance tree for an alignment file 2
FastME Distance-based inference of phylogenetic trees Phylogenetic tree analysis Phylogenetic tree generation (from molecular sequences) 4
Filter data on any column using simple expressions Formatting 1
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
Find-seq Align your sequences to new draft rice genomes 1
FisherBed calculate Fisher statistic between two feature files 17
FlankBed create new intervals from the flanks of existing intervals 18
folds create folds for classifiers evaluation through cross-validation 1
freak Residue/base frequency table or plot 4
fuzznuc Nucleic acid pattern search 5
fuzzpro Protein pattern search 4
fuzztran Protein pattern search after translation 4
garnier Predicts protein secondary structure 5
geecee Calculates fractional GC content of nucleic acid sequences 5
Genome Coverage compute the coverage over an entire genome 18
Get annotation statistics from VCF file 2
Get Haplotypes From Phased VCF 2
Get Subset of 3K VCF from Amazon S3 data repository 1
Get Unique Variety IDs/Assay ID 1
Get VCF of 3KRG from Amazon S3 bucket 1
Get-contig-names Extract contig or scaffold or chromosome names from rice genomes (draft and reference) 1
Get-subseq Extract sub-sequences from new draft rice genomes 1
GetFastaBed use intervals to extract sequences from a FASTA file 17
getorf Finds and extracts open reading frames (ORFs) 4
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
Haplophyle Generates haplotype network 2
HapmapToMLMMFiles converts a hapmap file into MLMM input files 2
helixturnhelix Report nucleic acid binding motifs 4
hmoment Hydrophobic moment calculation 4
iep Calculates the isoelectric point of a protein 4
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
infoseq Displays some simple information about sequences 5
Intersect multiple VCF datasets 3
Intersect intervals find overlapping intervals in various ways 17
isochore Plots isochores in large DNA sequences 4
JaccardBed calculate the distribution of relative distances between two files 17
Join two Datasets side by side on a specified field 3
LASSO predict phenotype using a LASSO approach 1
lindna Draws linear maps of DNA constructs 4
Line/Word/Character count of a dataset 1
LinksBed create a HTML page of links to UCSC locations 17
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
MapBed apply a function to a column for each overlapping interval 17
marscan Finds MAR/SAR sites in nucleic sequences 5
MaskFastaBed use intervals to mask sequences from a FASTA file 17
maskfeat Mask off features of a sequence 5
maskseq Mask off regions of a sequence 5
matcher Finds the best local alignments between two sequences 4
MDS plot IBS matrix / multi-dimensional scaling 3
megamerger Merge two large overlapping nucleic acid sequences 4
Merge multiple VCF datasets 3
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
merger Merge two overlapping nucleic acid sequences 4
MLMM GWAS using Multi-Locus Mixed-Model (MLMM) 1
MOL to CML 2
MOL to MOL2 2
MOL2 to CML 2
MOL2 to InChI 2
MOL2 to MOL 2
MOL2 to SDF 2
msbar Mutate sequence beyond all recognition 4
MultiCovBed counts coverage from multiple BAMs at specific intervals 17
Multiple Intersect identifies common intervals among multiple interval files 21
needle Needleman-Wunsch global alignment 4
newcpgreport Report CpG rich areas 4
newcpgseek Reports CpG rich region 4
newseq Type in a short new sequence 5
noreturn Removes carriage return from ASCII files 5
notseq Exclude a set of sequences and write out the remaining ones 5
nthseq Writes one sequence from a multiple set of sequences 4
NucBed profile the nucleotide content of intervals in a FASTA file 17
octanol Displays protein hydropathy 4
oddcomp Find protein sequence regions with a biased composition 4
OverlapBed computes the amount of overlap from two intervals 17
palindrome Looks for inverted repeats in a nucleotide sequence 4
Paste two files side by side 1
pasteseq Insert one sequence into another 4
patmatdb Search a protein sequence with a motif 5
Ped2Fasta Convert PED file to Fasta File 2
pepcoil Predicts coiled coil regions 4
pepinfo Plots simple amino acid properties in parallel 4
pepnet Displays proteins as a helical net 5
pepstats Protein statistics 5
pepwheel Shows protein sequences as helices 4
pepwindow Displays protein hydropathy 4
pepwindowall Displays protein hydropathy of a set of sequences 4
PLINK Filter large VCF file 2
plink: ped2bed Convert ped to bed 2
plot prediction shows scatterplot of a prediction vs true phenotype 1
plotcon Plot quality of conservation of a sequence alignment 4
plotorf Plot potential open reading frames 5
polydot Displays all-against-all dotplots of a set of sequences 4
prediction use machine learning model to predict phenotype from genotype 1
preg Regular expression search of a protein sequence 5
prettyplot Displays aligned sequences, with colouring and boxing 4
prettyseq Output sequence with translated ranges 4
primersearch Searches DNA sequences for matches with primer pairs 4
RandomBed generate random intervals in a genome 18
randomForest predict phenotype using a random forest approach 1
RAVE - Rapid Allelic Variant Extractor 2
Readseq Convert various alignment formats 2
ReldistBed calculate the distribution of relative distances 17
Remove beginning of a file 1
revseq Reverse and complement a sequence 5
Rooting Midpoint rooting of newick tree 3
Run PCA (Principal Component Analysis) on genetic data 1
SDF to CML 2
SDF to InChI 2
SDF to mol2 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
seqmatchall All-against-all comparison of a set of sequences 4
seqret Reads and writes sequences 5
SFF converter 1
showfeat Show features of a sequence 4
ShuffleBed randomly redistrubute intervals in a genome 18
shuffleseq Shuffles a set of sequences maintaining composition 4
sigcleave Reports protein signal cleavage sites 4
sirna Finds siRNA duplexes in mRNA 5
sixpack Display a DNA sequence with 6-frame translation and ORFs 5
skipseq Reads and writes sequences, skipping first few 4
Slice VCF to get data from selected regions 2
SlopBed adjust the size of intervals 18
sNMF Fast and efficient program for estimating individual ancestry coefficients 2
SNP density Calculate SNP densities along chromosome from a VCF input 3
SnpEff Variant effect and annotation 15
SnpSift Annotate SNPs from dbSnp 9
SnpSift CaseControl Count samples are in 'case' and 'control' groups. 9
SnpSift Filter Filter variants using arbitrary expressions 9
SnpSift Intervals Filter variants using intervals 9
SnpSift rmInfo remove INFO field annotations 7
SnpSift Variant Type Annotate with variant type 7
SnpSift vcfCheck basic checks for Vcf specification compliance 7
Sort data in ascending or descending order 2
SortBED order the intervals 17
SpacingBed reports the distances between features 13
splitter Split a sequence into (overlapping) smaller sequences 4
Subset columns from a VCF dataset 2
SubtractBed remove intervals based on overlaps 17
Summary Statistics for any numerical column 3
supermatcher Match large sequences against one or more other sequences 4
svm predict phenotype using a SVM approach 1
syco Synonymous codon usage Gribskov statistic plot 4
TagBed tag BAM alignments based on overlaps with interval files 17
Tassel Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. 1
tcode Fickett TESTCODE statistic to identify protein-coding DNA 4
textsearch Search sequence documentation. Slow, use SRS and Entrez! 5
tmap Displays membrane spanning regions 5
tranalign Align nucleic coding regions given the aligned proteins 5
transeq Translate nucleic acid sequences 5
Trim leading or trailing characters 1
trimest Trim poly-A tails off EST sequences 4
trimseq Trim ambiguous bits off the ends of sequences 4
twofeat Finds neighbouring pairs of features in sequences 4
union Reads sequence fragments and builds one sequence 5
Uniqprimer Design specific primers of sequences 2
Upload File from your computer 2
VCF to Hapmap Convert VCF to Hapmap 2
VCF to MAF Custom Track for display at UCSC 1
VCF tools SlidingWindow Make diversity computation with sliding window 3
VCFtools Filter 3
VCFtools Stats 4
vectorstrip Strips out DNA between a pair of vector sequences 4
water Smith-Waterman local alignment 4
Wig/BedGraph-to-bigWig converter 2
Wiggle to Interval 1
WindowBed find overlapping intervals within a window around an interval 17
wobble Wobble base plot 4
wordcount Counts words of a specified size in a DNA sequence 4
wordmatch Finds all exact matches of a given size between 2 sequences 4