734 tool(s) found

Tool Description Topics Available version(s)
464 C01 - evaluate 1
464 GUANINE Reporter 1
[5.15-54.0] Interproscan functional predictions of ORFs Interproscan functional predictions of ORFs 2
[5.22-61.0] Interproscan functional predictions of ORFs Interproscan functional predictions of ORFs 1
aaChanges amino-acid changes caused by a set of SNPs 2
ABIF Info Dump information about AB1 file 1
Access Assessment 1 Organism via IFrame to Apollo 1
Access Assessment 2 Organism via IFrame to Apollo 1
Add column to an existing dataset 3
Add Terminal Repeats to a GenBank file with one or more genomes 1
Add Terminal Repeats to a Genbank file with one or more genomes 1
AddCommentsToBam add comments to BAM dataset 11
AddOrReplaceReadGroups add or replaces read group information 11
addstring2fashead Converts fasta file with sequences from same species and gene family to phytab format 1
Aggregate datapoints Appends the average, min, max of datapoints per interval 1
alimask append modelmask line to a multiple sequence alignments 5
Amino Acid Positional Information for an input GBK file 1
Analyse TerL Sequences Analyse sequences for similarity to known TerL sequences, assigning a morphology based on homology 1
Annotate a VCF dataset with custom filters 2
Annotate opens an IFrame to Apollo 1
AnnotateBed annotate coverage of features from multiple files 17
Annotation Table from gff3 formatted datasets 1
antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar. 4
Aragorn detect tRNA genes in nucleotide sequences 1
ART 454 simulates pyrosequencing data 1
ART Illumina simulates sequencing data 1
ART SOLiD simulates SOLiD data 1
Auto-reopen attempts to automatically re-open phage genomes based on various heuristics. 1
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
backtranseq Back translate a protein sequence 5
Bacterial Codon Frequencies Database spits out a list of codon frequencies from the CPT's bacterial codon frequency database 1
BAM to BED converter 21
BAM to BigWig Calculates coverage from a BAM alignment file 4
BAM-to-SAM convert BAM to SAM 8
bamCompare normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig) 2
bamCorrelate correlates pairs of BAM files 2
bamCoverage generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig) 2
bamFingerprint plots profiles of BAM files; useful for assesing ChIP signal strength 2
bamPEFragmentSize Given a BAM file it samples several regions to estimate the paird-end fragment length 2
banana Bending and curvature plot in B-DNA 5
Bar chart for multiple columns 1
Barcode Splitter 6
BaseSpace Auth Part 1 1
BaseSpace Auth Part 2 1
BaseSpace: List Runs 1
BaseSpace: List Samples 1
BaseSpace: Sample Downloader 1
BaseSpace: Single Sample Downloader 1
BCF Tools Cat This tool allows the user to concatenate BCF files. 3
BCF Tools Index This tool allows the user to index sorted BCF for random access. 3
bcftools call SNP/indel variant calling from VCF/BCF 7
bcftools view VCF/BCF conversion, view, subset and filter VCF/BCF files 9
BEAST 1.7.2 Bayesian evolutionary analysis by sampling trees. 1
beautifyfasta Converts interleaved fasta to non-interleaved 1
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
BedToIntervalList convert coordinate data into picard interval list format 11
bigwigCompare normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference 2
Bin Fasta Sequences to reach a target length 1
Bin Fasta Sequences - Postprocess into separate collections 1
biosed Replace or delete sequence sections 5
BLASR The PacBio(R) long read aligner 1
Blast Tabular Add Dice adds dice score to last column 1
Blast Tabular Dice Filter removes low-dice blast results 1
Blast TSV to Protein XMFA 1
BLAST XML to tabular Convert BLAST XML output to tabular Conversion 16
blast2html Convert BLAST XML to HTML 1
blast2html-split Convert BLAST XML to HTML split into separate files 1
blastclust Cluster proteins with blast 1
BlastClust Fasta Separator separated clusters into individual fasta files 1
BlastN TSV to gapped GFF3 converts tabular blast results to a JBrowse-compatible file 1
BlastXML NT to gapped GFF3 converts nucleotide blast results to a JBrowse-compatible file 1
BlastXML to gapped GFF3 converts blast results to a JBrowse-compatible file 1
Bowtie2 - map reads against reference genome 22
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
Canu assembler Assembler optimized for long error-prone reads such as PacBio, Oxford Nanopore 1
Cassette ID Generator calculate cassette ID string for genomes 1
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
chaos Create a chaos game representation plot for a sequence 5
charge Protein charge plot 4
Charges colour sequences based on rules 1
checktrans Reports STOP codons and ORF statistics of a protein 4
chips Codon usage statistics 5
CID Scoring produces from-to-score table of CIDS for input CID table 1
Circos visualizes data in a circular layout 3
Circos based DNAPlotter plots genomes similar to Artemis's DNAPlotter 1
cirdna Draws circular maps of DNA constructs 5
CleanSam perform SAM/BAM grooming 11
Clip adapter sequences 5
ClosestBed find the closest, potentially non-overlapping interval 17
Clustal Omega multiple sequence alignment program for proteins 1
ClustalW multiple sequence alignment program for DNA or proteins 4
ClusterBed cluster overlapping/nearby intervals 17
CML to InChI 2
CML to mol2 2
CML to SDF 2
CML to SMILES 2
codcmp Codon usage table comparison 5
coderet Extract CDS, mRNA and translations from feature tables 5
Codon Usage summarise codon usage from a GFF3 annotation of a genome 1
Cofold An RNA secondary structure prediction method that takes co-transcriptional folding into account 1
Collapse sequences 4
Collect Alignment Summary Metrics writes a file containing summary alignment metrics 11
CollectBaseDistributionByCycle charts the nucleotide distribution per cycle in a SAM or BAM dataset 11
CollectGcBiasMetrics charts the GC bias metrics 11
CollectInsertSizeMetrics plots distribution of insert sizes 11
Collector’s curve of sequencing yield over time 1
CollectRnaSeqMetrics collect metrics about the alignment of RNA to various functional classes of loci in the genome 12
CollectWgsMetrics compute metrics for evaluating of whole genome sequencing experiments 11
Color Add a `/color` tag to GenBank files based on text in the `/product` field. 1
Column Join 1
Column Regex Find And Replace 3
Columnar Data Comparison generates a comparison map of two datasets 1
Columnar Data Rescale and Partitioning transforms data sets according to a particular modification type to coerce them for use in downstream analysis 1
Columnar Data Transformation apply mathetmatical transformations to datasets 1
Combine FASTA and QUAL into FASTQ 3
Compare multiple VCF datasets 2
Compare Codon Usage between two genomes 1
Compare two Datasets to find common or distinct rows 1
Comparison Mapper utilising multiple sets of input data as a basis for generating a comparison matrix which can then be fed into the clustering tool 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 quality statistics 4
Compute quality statistics for SOLiD data 1
Compute sequence length 5
computeGCBias to see whether your samples should be normalized for GC bias 2
computeMatrix summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile 2
Concatenate datasets tail-to-head 1
Concatenate Fasta Sequences merge into single long sequence 1
Concatenate multiple datasets tail-to-head 1
Concatentate multiple files into a single file 1
Contig Coverage produces a table of coverage levels per contig 1
Convert delimiters to TAB 1
Convert SOLiD output to fastq 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 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
Convert XMFA to BigWig track 1
Convert XMFA to gapped GFF3 1
Convert XMFA to percent identity table 1
Correct Apollo exons to SD 1
Correct GeneMarkS Gene Model 1
correctGCBias uses the output from computeGCBias to generate corrected BAM files 2
Count occurrences of each record 2
cpgplot Plot CpG rich areas 5
cpgreport Reports all CpG rich regions 4
Create assemblies with Unicycler 7
Create or Update Organism will create the organism if it doesn't exist, and update otherwise 1
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
cusp Create a codon usage table 5
Cut columns from a table 2
cutseq Removes a specified section from a sequence 4
dan Calculates DNA RNA/DNA melting temperature 4
Deduplicate file Removes duplicate lines 1
degapseq Removes gap characters from sequences 5
Delete all annotations from an Apollo record 1
descseq Alter the name or description of a sequence 5
DESeq Determines differentially expressed transcripts from read alignments 3
DESeq2 Differential gene expression analysis based on the negative binomial distribution 2
DEXSeq Inference of differential exon usage in RNA-Seq 2
diffseq Find differences between nearly identical sequences 4
digest Protein proteolytic enzyme or reagent cleavage digest 5
Disambiguate ambiguous sequences produces random, unambiguous variants of ambiguous sequences 1
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
Downsample SAM/BAM Downsample a file to retain a subset of the reads 11
Draw nucleotides distribution chart 4
Draw quality score boxplot for SOLiD data 1
dreg Regular expression search of a nucleotide sequence 5
EFetch 1
einverted Finds DNA inverted repeats 4
epestfind Finds PEST motifs as potential proteolytic cleavage sites 4
equicktandem Finds tandem repeats 4
est2genome Align EST and genomic DNA sequences 4
EstimateLibraryComplexity assess sequence library complexity from read sequences 11
etandem Looks for tandem repeats in a nucleotide sequence 4
EvolMAP Runs EvolMAP. 1
EvolMAP Long Runs EvolMAP for longer (bigger) jobs. 1
EvolMAP Output Species Exclude Modifies EvolMAP Output to exclude specific species. 1
EvolMAP Output to FASTA Converts EvolMAP Output file to FASTA file 1
EvolMAP Output Tool Modifies EvolMAP output 1
ExpandBed replicate lines based on lists of values in columns 17
Extract Authorship from GenBank File 1
Extract CD-HIT clusters into Dataset Collection 1
Extract CD-HIT Clusters Sizes 1
Extract FASTQ in tabular format from a set of FAST5 files 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 nanopore events from a set of sequencing reads 1
Extract Pairwise MAF blocks given a set of genomic intervals 1
Extract Qualifers Extract feature qualifier values into table 1
Extract reads in FASTA or FASTQ format from nanopore files 1
Extract time and channel information from a set of FAST5 files 1
extractfeat Extract features from a sequence 4
extractseq Extract regions from a sequence 5
FASConcat Appends all input sequence files into one file 1
Fasta AA Stats Calculate AA frequencies in sequences 1
Fasta Codon Optimiser optimizes codons for a particular host bacteria 1
Fasta Codon Stats calculates codon frequencies in sequences 1
Fasta Deduplicator removes duplicate sequences from a fasta file 1
Fasta Extract Sequence Extract a single sequence from a fasta file. 1
Fasta Length Table calculates sequence lengths 1
FASTA Regex Search Filter sequences based on regular expressions 1
Fasta Sequence Calculator calculates commonly used sequence properties like GC skew, hydrophilicity, etc 1
Fasta Sequence Joiner find sequences in common 1
Fasta Sequence Renamer rename fasta sequences 1
Fasta Translate Translate fasta file 1
FASTA Validator checks FASTA files for formatting, duplicate sequences, and duplicate IDs 1
FASTA Width formatter 4
FASTA-to-Tabular converter 3
fasta2phylipE Convert Aligned FASTA to phylip Extended 1
FASTQ Groomer convert between various FASTQ quality formats 4
FastQ Subset reduce results for X-fold coverage 1
FASTQ to FASTA converter 4
FastQC Read Quality reports Sequence composition calculation Sequencing quality control Statistical calculation 17
FastqToSam convert Fastq data into unaligned BAM 14
Feature Sequence Export Unique specially modified for sending CDSs to blast 1
Fetch Annotation Set for an organism from CACAO 1
Filter data on any column using simple expressions Formatting 1
Filter BlastXML based on e-value and hit position 1
Filter GenBank Features based on specific tags/qualifiers from a GenBank file 1
Filter MAF by specified attributes 1
Filter MAF blocks by Size 1
Filter MAF blocks by Species 1
Filter sequences by length Filtering 5
Filter SPAdes output remove low coverage and short contigs/scaffolds 1
Filter top N blast results 1
FilterSamReads include or exclude aligned and unaligned reads and read lists 11
FIMO - Find Individual Motif Occurrences 9
Find and replace text from a dataset 1
find in reference filter peptides that are present in proteins 3
Find L-like proteins Finds L-like proteins in fasta file 1
FindSpanin does what it says on the tin 1
FisherBed calculate Fisher statistic between two feature files 17
Fix Aragorn tRNA model 1
Fix Gene Boundaries to include RBS based on locus_tag 1
FixMateInformation ensure that all mate-pair information is in sync between each read and it's mate pair 11
FlankBed create new intervals from the flanks of existing intervals 18
Format cd-hit outputs to rename representative sequences with cluster name and/or extract distribution inside clusters given a mapping file 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
gblocks Convert Aligned FASTA to phylip Extended Sequence masking 2
geecee Calculates fractional GC content of nucleic acid sequences 5
GenBank Feature Array Plot plots features as an array of colored boxes 1
GenBank Feature Comparison compare feature locations 1
GenBank Feature Export Export a subset of features from a GenBank file 1
GenBank Gene Model Correction adds genes when only CDSs are annotated 1
Genbank Genome Information calculates various statistics and information about a genbank file 1
GenBank Genome Sequence Export export sequence from GenBank files as fasta 1
GenBank Metadata Export exports metadata about GenBank files (citations, taxonomy, etc) 1
GenBank Source Extractor Extract host genus & species from GenBank files 1
Genbank to Five Column Format 1
Genbank to GFF3 converter 2
Gene BED To Exon/Intron/Codon BED expander 1
GeneMarkS GeneMarkS 1
Generate all possible SNPs in fasta files 1
Generate Assessment 1 Organism 1
Generate box-whisker plot of quality score distribution over positions in nanopore reads 1
Generate histogram of nanopore read lengths 1
Generate pileup from BAM dataset 3
Genome Coverage compute the coverage over an entire genome 18
Genome Editor allows you to re-arrange a genome 1
Genome Mapper 1
Genome Randomizer 1
Get longest read from a set of FAST5 files. 1
Get open reading frames (ORFs) or coding sequences (CDSs) e.g. to get peptides from ESTs 5
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
GFF3 Add Gene to CDS is one step of fixing a gene model--adding parent gene features to CDSs 1
GFF3 Color colors gff3 features based on product tags 1
GFF3 Contained Location Filter Extract gff3 features which contain one or more locations 1
GFF3 Extract Introns Extracts intron features from genes with multiple CDSs 1
GFF3 Feature Sequence Export Export corresponding sequence in genome from GFF3 1
GFF3 Feature Type Filter selects features from a gff3 file based on feature type 1
GFF3 Filter filter gff3 features based on qualifier value 1
GFF3 Filter: Require Phage Start ensures start is ATG, TTG, or GTG 1
Gff3 Filter: Require SD ensures CDSs have an SD 1
GFF3 Fix NCBI gff for Apollo 1
GFF3 Location Filter filter gff3 features based on location 1
GFF3 Parent Child Feature Map 1
GFF3 to Apollo Annotations 1
GFF3 to GenBank convert gff3 to GenBank 1
Glimmer ICM builder 2
Glimmer3 Predict ORFs in prokaryotic genomes (knowlegde-based) 2
Glimmer3 Predict ORFs in prokaryotic genomes (not knowlegde-based) 2
Glimmer3 to GFF3 convert formats 1
Group data by a column and perform aggregate operation on other columns. 3
Group Sequences group sequences according to user queries 1
GroupByBed group by common cols and summarize other cols 17
GSAF Download downloads data from UT's GSAF 1
GTF-to-BEDGraph converter Conversion 1
heatmapper creates a heatmap for a score associated to genomic regions 2
helixturnhelix Report nucleic acid binding motifs 4
Hidden Stop Codon Detector detects +1/-1 stop codons 1
Hierarchical Clustering runs R stat module's hclust algorithm 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
hmoment Hydrophobic moment calculation 4
iAssembler Assembly of transcriptomes. 1
Identify Lipoboxes in protein sequences 1
iep Calculates the isoelectric point of a protein 4
IlluQC Parallel Runs IlluQC Parallel verion 1
InChI to CML 2
InChI to MOL 2
InChI to MOL2 2
InChI to SDF 2
InChI to SMILES 2
infoseq Displays some simple information about sequences 5
Intersect multiple VCF datasets 3
Intersect two gff3 files. Only top-level features 1
Intersect intervals find overlapping intervals in various ways 17
Intersect Tabular Files based on a shared column (Inner Join) 1
Intron Detection based on nearby protein blast results 1
iReport create an HTML report 2
isochore Plots isochores in large DNA sequences 4
JaccardBed calculate the distribution of relative distances between two files 17
jackhmmer iteratively search a protein sequence against a protein database (PSIBLAST-like) 5
JBrowse genome browser 11
JBrowse 0.6.3+cpt genome browser 1
JModelTest 1.0 JModelTest description here. 1
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 Scoring produces from-to-score table of lengths for input length table (CPT LOGS) 1
Ligate Fasta Sequences with common and custom adapter sequences 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
LipoP program for prediction of lipoproteins and for discriminating between lipoprotein signalpetides, other signal peptides and n-terminal membrane helices in Gram negative bacteria. 1
List Organism Data from Apollo 1
List Organisms in Apollo 1
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
mafft Multiple Sequence Alignment 2
MakeWindowsBed make interval windows across a genome 18
Map with BFAST 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
Map with Mosaik 1
Map with PerM for SOLiD and Illumina 1
MapBed apply a function to a column for each overlapping interval 17
MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules 11
MarkDuplicatesWithMateCigar examine aligned records in BAM datasets to locate duplicate molecules 11
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
Mauve Alignment Graph from XMFA backbone 1
MeanQualityByCycle chart distribution of base qualities 11
megamerger Merge two large overlapping nucleic acid sequences 4
MEME - Multiple Em for Motif Elicitation 10
Merge multiple VCF datasets 3
Merge BedGraph files combines coverage intervals from multiple BEDGRAPH files 17
Merge Columns together 2
Merge LCBs within a given threshold distance 1
MergeBamAlignment merge alignment data with additional info stored in an unmapped BAM dataset 11
MergeBED combine overlapping/nearby intervals into a single interval 17
merger Merge two overlapping nucleic acid sequences 4
MergeSamFiles merges multiple SAM/BAM datasets into one 11
MetaGeneAnnotator MetaGeneAnnotator is a gene-finding program for prokaryote and phage. 1
MGA to GFF3 1
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
MIST v3 Multiple Interrelated Sequence doT plotter. 1
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
MPileup call variants 10
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
MUMmer : Compare genomes (Nucmer or Promer) 1
MUMmer Clustering : order sequence matches in clusters 1
MUMmer MaxMatch : Maximal exact sequence matching 1
MUMmer plot : Generate MUMmerplots from MUMmer match file 1
MUMmer utilities : Show and filter on sequence delta file 1
MUMmer2ACT : convert MUMmer comparison (coords) file to ACT (Artemis) 1
Nanopolish eventalign - Align nanopore events to reference k-mers 2
Nanopolish methylation - Classify nucleotides as methylated or not. 2
Nanopolish variants - Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences 2
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
Nearby features in two gff3 files 1
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
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
NJst Estimate species tree with NJst from table of tree names and newick trees 1
NONE Validator 1
noreturn Removes carriage return from ASCII files 5
NormalizeFasta normalize fasta datasets 11
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
One SNP Away Finds residues that are one SNP away from input amino acid 1
OverlapBed computes the amount of overlap from two intervals 17
PacBio Read Dataset Generator creates Galaxy dataset from input hdf5 files 1
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
PAUSE BAM to Starts Wiggle create wiggle file from starts information 1
PDpairs Pairwise distance between taxa in a phylogenetic tree 1
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
PHACTS simple and automated classification of phage lifestyles 1
Phage Frame Shift Finder finds possible frame shifts 1
Phage QC validate phage annotations 1
Phage Renamer renames genbank files based on their record names and CPT Regex Rules. 1
PhageTerm PhageTerm: a Fast and User-friendly Software to Determine Bacteriophage Termini and Packaging Mode using randomly fragmented NGS data. Read mapping 2
phmmer search a protein sequence against a protein database (BLASTP-like) 5
Phylobayes Runs phylobayes 1
Phylocatenator Produces concatenated sequence file from phytab file of aligned sequences 1
Phylomatic Run Phylomatic 1
phyloP interspecies conservation scores 1
Phyogenetic reconstruction with RaXML - Maximum Likelihood based inference of large phylogenetic trees 3
phytab aliscorecut aliscorecut :: Runs Aliscore then Alicut on an aligned sequence from phytab Muscle. 1
phytab clearcut clearcut: Generate Neighbor Joining phylogeny. Input can be fasta or phytab format. 1
phytab HMMBUILD hmmbuild :: profile HMM construction from multiple sequence alignments in phytab format. 1
PHYTAB HMMSEARCH hmmsearch :: search profile(s) against a sequence database. Produces a phytab output. 1
phytab LB pruner LB_pruner: Identify genes on very long branches. 1
PHYTAB MUSCLE MUSCLE: Multiple sequence alignment. Input can be fasta or phytab format. 1
PHYTAB prank prank: Multiple sequence alignment. Input can be fasta or phytab format. 1
Phytab RaXML Phytab RaXML - RaXML for phytab format 1
Phytab RaXML pars Phytab RaXML - RaXML for phytab format 1
Pileup-to-Interval condenses pileup format into ranges of bases 5
pilon An automated genome assembly improvement and variant detection tool 2
place_fossils Maximum Likelihood Analysis 1
Plot performance per cell in nanopore reads 1
Plot signals for nanopore reads 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
PPEPP Paradigm Phage Early Promoter Project. Finds promoters that ought to be expressed by unmodified host RNA polymerase, utilising HMMR3 databases curated from T3, T5, T7, P1, P2, P4, and 186 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
profiler creates a profile plot for a score associated to genomic regions 2
progressiveMauve constructs multiple genome alignments 1
prottest Selection of best-fit models of protein evolution. 1
Prune_taxa Pruning taxa from a tree or multiple trees 1
PSM Comparison Table aligns and lists data from PSM Prep 1
PSM Plotter plots data from PSM Prep 1
PSM Prep prepares data for the PSM Plotter 1
QualityScoreDistribution chart quality score distribution 11
Quast Genome assembly Quality 5
RandomBed generate random intervals in a genome 18
RAxML read placement RAxML read placement - Produces a labeled tree from RAxML. 1
raxml_pars Use RAxML to calculate a phylogeny with Parsimony 1
Re-align with SRMA 1
Read length statistics from a set of FAST5 files 1
Rebase GFF3 features against parent features 2
Rebase Wig Analysis Results against parent features 1
Reformat GFF3 File by passing it through biopython 1
Regex Find And Replace 2
Register Annotation Set registers an organism and gene call set with CACAO for annotation. 1
Relabel Genbank Tags re-labels genbank tags according to rules 1
Related Genomes based on PHAGE blast results 1
Related Genomes based on nucleotide blast results 1
Related Genomes based on protein blast results 1
ReldistBed calculate the distribution of relative distances 17
Remove Annotation Feature that's unused in our GFF tools 1
Remove beginning of a file 1
Remove Description from fasta file 1
Remove GenBank Features removes specific features from a GenBank file 1
Remove GenBank Tags removes specific tags/qualifiers from a GenBank file 1
Remove sequencing artifacts 5
Rename features in Apollo 1
Rename Sequence allows you to change ID in genbank, gff3, and fasta files. 1
Rename sequences 5
Renumber GenBank Genes relabels/renumbers GenBank tags according to rules 1
Reopen a gff3 file (and optional fasta file) at a specific location 1
Reopen Contig Reopen Genbank file in a new location 1
Reopen Fasta Sequences at specific location 1
ReorderSam reorder reads to match ordering in reference sequences 14
ReplaceSamHeader replace header in a SAM/BAM dataset 14
reprof protein secondary structure and accessibility prediction 2
Retrieve Data from Apollo into Galaxy 1
Retrieve JBrowse for an organism, from Apollo 1
Reverse and Complement a gff3 file (and optional fasta file) 1
Reverse and Complement Fasta Files 1
Reverse and Complement GenBank Files 1
Reverse Complement a MAF file 1
reverse complement of DNA/RNA sequences 1
Reverse-Complement 5
RevertOriginalBaseQualitiesAndAddMateCigar revert the original base qualities and add the mate cigar tag 11
RevertSam revert SAM/BAM datasets to a previous state 11
revseq Reverse and complement a sequence 5
RmDup remove PCR duplicates 8
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
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
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
Safely Reopen Fasta based on gene calls 1
SAM-to-BAM convert SAM to BAM 11
SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq 14
Scythe Scythe - A very simple adapter trimmer. 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
seqmatchall All-against-all comparison of a set of sequences 4
seqret Reads and writes sequences 5
seqtk_comp get the nucleotide composition of FASTA/Q 3
seqtk_cutN cut sequence at long N 3
seqtk_dropse drop unpaired from interleaved Paired End FASTA/Q 3
seqtk_fqchk fastq QC (base/quality summary) 3
seqtk_hety regional heterozygosity 3
seqtk_listhet extract the position of each het 3
seqtk_mergefa merge two FASTA/Q files 3
seqtk_mergepe interleave two unpaired FASTA/Q files for a paired-end file 3
seqtk_mutfa point mutate FASTA at specified positions 3
seqtk_randbase choose a random base from hets 3
seqtk_sample random subsample of fasta or fastq sequences 3
seqtk_seq common transformation of FASTA/Q 3
seqtk_subseq extract subsequences from FASTA/Q files 3
seqtk_trimfq trim FASTQ using the Phred algorithm 3
Sequence Gap Remover Removes gap in sequences 1
Sequence Logo generator for fasta (eg Clustal alignments) 3
Sequin generates files which can be sent to NCBI for genome submission 1
SFF converter 1
Sff2FastQ Convert SFF files to FastQ files 1
Share Organism With User in Apollo 1
ShineFind v1.5 Identify shine-dalgarno sequences 1
Show nucleotide distribution in nanopore sequencing reads 1
Show quality score distribution in nanopore sequencing reads 1
showfeat Show features of a sequence 4
SHtest Use RAxML to calculate SHtest to compare trees 1
ShuffleBed randomly redistrubute intervals in a genome 18
shuffleseq Shuffles a set of sequences maintaining composition 4
sigcleave Reports protein signal cleavage sites 4
SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. 1
SignalP to GFF3 converts txt formatted SignalP to gff3 results 1
SignalP+Fasta processing uses SignalP output and original fasta sequence to process out various portions of the SignalP results for use later 1
Similar Sequence Remover Removes characters in a sequence 1
Simple Primer Generator 1
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
SMILES to CML 2
SMILES to InChI 2
SMILES to MOL 2
SMILES to MOL2 2
SMILES to SDF 2
SMILES to SMILES 2
SNP Plot simple plot of generated snps against a reference sequence 1
Sort data in ascending or descending order 2
SortBED order the intervals 17
SortSam sort SAM/BAM dataset 11
SPAdes genome assembler for regular and single-cell projects 10
SPAdes stats coverage vs. length plot 1
Split col 25 BLAST results to create a unique entry per subject title 1
Split Genbank File Splits a multi-genbank file into separate genbank files 1
Split GFF3 into reading frames Splits GFF3 file into 6 files according to gene reading frames 1
Split GFF3+Fasta into separate parts 1
Split LCBs into smaller LCBs 1
Split MAF blocks by Species 1
Split/Duplicate NCBI headers 1
SplitFasta 2
splitter Split a sequence into (overlapping) smaller sequences 4
Start and SD scrubber Breaks starts and SDs when possible 1
Start Codon Statistics Extract a table of start codon frequencies from a Genbank file 1
Start Codon Statistics Summarise start codon usage 1
Start Codon Statistics Summarise start codon usage 1
Stitch Gene blocks given a set of coding exon intervals 1
Stitch MAF blocks given a set of genomic intervals 1
Stop Codon Statistics Extract a table of stop codon frequencies from a Genbank file 1
Stop Codon Statistics Summarise stop codon usage 1
Stop Codon Statistics Summarise stop codon usage 1
Subsection of GenBank file allows you to extract range/subsection/segment/subset from GenBank files 1
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
syco Synonymous codon usage Gribskov statistic plot 4
tab2trees Create pdf of phylogeny graphics from table of tree names and newick trees 1
tab_collapse collapse tabular files 1
Tabular-to-FASTA converts tabular file to FASTA format 2
Tabular-to-HTML for easier table viewing 1
TagBed tag BAM alignments based on overlaps with interval files 17
Tagdust TagDust - A program to eliminate artifactual reads from next-generation sequencing data sets. 1
tcode Fickett TESTCODE statistic to identify protein-coding DNA 4
textsearch Search sequence documentation. Slow, use SRS and Entrez! 5
Thinning_trees Sub-sample trees from from a posterior distribution 1
tmap Displays membrane spanning regions 5
TMHMM predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. 1
TMHMM (GFF3) for prediction of transmembrane helices in proteins 1
TMHMM+Fasta processing uses TMHMM output and original fasta sequence to process out various portions of the TMHMM results for use later 1
tnt2table Converts TNT text output from Morphobank into UCSB-phylotable. 1
Top Hits Table based on blast tabular files 1
tranalign Align nucleic coding regions given the aligned proteins 5
transeq Translate nucleic acid sequences 5
Translate Runs Translate 1
TransTermHP predicts transcription terminators 1
tree_support Calculates support for nodes of a single tree (bootstrap) using a file of multiple trees 1
TreeVector Draw a Phylogenic Tree 1
Trim leading or trailing characters 1
Trim sequences 6
trimest Trim poly-A tails off EST sequences 4
trimseq Trim ambiguous bits off the ends of sequences 4
tRNA and tmRNA prediction (Aragorn) 3
twofeat Finds neighbouring pairs of features in sequences 4
UCSB Hamster UCSB Hamster is a Galaxy port for the Hamster script which finds orthologs based on HMM's. 1
union Reads sequence fragments and builds one sequence 5
Update Assessment 1 Results 1
ValidateSamFile assess validity of SAM/BAM dataset 11
VarScan for variant detection 3
VarScan2 Call INDELs from a mpileup file VarScan2 INDEL detection (on mpileup data) 2
VarScan2 Call INDELs from BAM VarScan2 INDEL detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance. 2
VarScan2 Call SNPs from a mpileup file VarScan2 SNP/SNV detection; directly from a *.mpileup file. 2
VarScan2 Call SNPs from BAM VarScan2 SNP/SNV detection; directly reading *.bam file(s) & using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance. 2
VCF to MAF Custom Track for display at UCSC 1
vectorstrip Strips out DNA between a pair of vector sequences 4
velvetg Velvet sequence assembler for very short reads 4
velveth Prepare a dataset for the Velvet velvetg Assembler 4
velvetoptimiser Auto optimise a genomic velvet assembly 4
vert_tree_format Convert between phylogenetic tree file formats 1
Virtual Suppressor Strain generates a genome with specified stop codons suppressed 1
Virtual Suppressor Strain suppresses stop codons 1
water Smith-Waterman local alignment 4
Wig to BigWig CPT version accepts fasta input for genome lengths. 1
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
X-Vis from XMFA file 1
XPath compute xpath expressions on XML data 2