Galaxy Tools

Validate Study XML

Validate Sample XML

Validate Experiment XML

Validate Run XML

Validate Analysis XML

Browse Genboree

Download from Genboree

Upload to Genboree

Validate an lff file

LFF-to-BED converter

LFF-to-GFF converter

BED-to-LFF converter

GFF-to-LFF converter

Read Mapping Using Pash 3.0 Map short reads onto a reference human genome

Convert Pash output to BED format Convert Pash output into BED format

ChIP-Seq Peaks Detection Perform ChIP-Seq peak analysis and generate results in the format of Genboree Lff Tracks

Interpret ChIP-Seq Peaks Assist with interpretation of ChIP-Seq results

Small RNA Seq Mapping Using Pash 3.0 Map short reads onto a reference human genome

Interpret small RNA-Seq Peaks Assist with interpretation of small RNA-Seq results

Bisulfite Read Mapping Using Pash 3.0 Map bisulfite treated short reads onto reference genome using Pash 3.0.

PCR primer design using primer3 and isPCR Design PCR primers using primer3 and isPCR

Structural variants intersection SV coverage between query and target tracks

SV comparison with published datasets SV coverage of a query sv-lff file for multiple target tracks

svlff2csv tool export to TAB delimited format

csv2svlff tool convert to svLff format

BRL Enrichment Tool BRL Enrichment

Upload File from your computer

UCSC Main table browser

UCSC Archaea table browser

Get Microbial Data

BioMart Central server

C. Elegans server

Flymine server

EncodeDB at NHGRI

HbVar Human Hemoglobin Variants and Thalassemias

Convert genome coordinates between assemblies and genomes

Add column to an existing query

Compute an expression on every row

Concatenate queries tail-to-head

Condense consecutive characters

Convert delimiters to TAB

Create single interval as a new query

Cut columns from a table

Change Case of selected columns

Paste two files side by side

Remove beginning of a file

Select first lines from a Query

Select last lines from a Query

Filter data on any column using simple expressions

Sort data in ascending or descending order

Select lines that match an expression

Join two Queries side by side on a specified field

Compare two Queries to find common or distinct rows

Subtract Whole Query from another query

Group data by a column and perform aggregate operation on other columns.

AXT to concatenated FASTA Converts an AXT formated file to a concatenated FASTA alignment

AXT to FASTA Converts an AXT formated file to FASTA format

AXT to LAV Converts an AXT formated file to LAV format

BED-to-GFF converter

BED-to-LFF converter

FASTA-to-Tabular converts FASTA file to tabular format

FASTQSOLEXA-to-FASTA-QUAL extracts sequences and quality scores from FASTQSOLEXA data

GFF-to-BED converter

GFF-to-LFF converter

LAV to BED Converts a LAV formated file to BED format

LFF-to-BED converter

LFF-to-GFF converter

Maf to BED Converts a MAF formated file to the BED format

Maf to FASTA Converts a MAF formated file to FASTA format

Tabular-to-FASTA converts tabular file to FASTA format

Gene BED To Exon/Intron/Codon BED expander

Extract features from GFF file

Extract Genomic DNA using coordinates from assembled/unassembled genomes

Wiggle-to-Interval converter

Aggregate datapoints such as phastCons, GERP, binCons, and others for a set of genomic intervals

Compute phastOdds score for each interval

Intersect the intervals of two queries

Subtract the intervals of two queries

Merge the overlapping intervals of a query

Concatenate two queries into one query

Base Coverage of all intervals

Coverage of a set of intervals on second set of intervals

Complement intervals of a query

Cluster the intervals of a query

Join the intervals of two queries side-by-side

Get flanks returns flanking region/s for every gene

Fetch closest feature for every interval

Profile Annotations for a set of genomic intervals

RME module search Takes a binary matrix and finds modules that have patterns of recurrence and mutual exclusivity.

Summary Statistics for any numerical column

Count occurrences of each record

Correlation for numeric columns

Histogram of a numeric column

Scatterplot of two numeric columns

Plotting tool for multiple series and graph types

GMAJ Multiple Alignment Viewer

LAJ Pairwise Alignment Viewer

Build custom track for UCSC genome browser

Make windows

Feature coverage

Filter nucleotides based on quality scores

Mask CpG sites from MAF file

Fetch Indels from pairwise alignments

Fetch Indels from 3-way alignments

Estimate Indel Rates for 3-way alignments

Fetch substitutions from pairwise alignments

Estimate substitution rates for non-coding regions

Extract Orthologous Microsatellites from pair-wise alignments

Estimate microsatellite mutability by specified attributes

Perform Linear Regression

Perform Best-subsets Regression

Compute RCVE

Branch Lengths Estimation

Neighbor Joining Tree Builder

dN/dS Ratio Estimation

Fetch taxonomic representation

Summarize taxonomy

Draw phylogeny

Find diagnostic hits

Poisson two-sample test

antigenic Predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.

backtranseq Back translate a protein sequence

banana Bending and curvature plot in B-DNA

biosed Replace or delete sequence sections

btwisted Calculates the twisting in a B-DNA sequence

cai custom CAI codon adaptation index using custom codon usage file

cai CAI codon adaptation index

chaos Create a chaos game representation plot for a sequence

charge Protein charge plot

checktrans Reports STOP codons and ORF statistics of a protein

chips Codon usage statistics

cirdna Draws circular maps of DNA constructs

codcmp Codon usage table comparison

coderet Extract CDS, mRNA and translations from feature tables

compseq Count composition of dimer/trimer/etc words in a sequence

cpgplot Plot CpG rich areas

cpgreport Reports all CpG rich regions

cusp Create a codon usage table

cutseq Removes a specified section from a sequence

dan Calculates DNA RNA/DNA melting temperature

degapseq Removes gap characters from sequences

descseq Alter the name or description of a sequence

diffseq Find differences between nearly identical sequences

digest Protein proteolytic enzyme or reagent cleavage digest

dotmatcher Displays a thresholded dotplot of two sequences

dotpath Non-overlapping wordmatch dotplot of two sequences

dottup Displays a wordmatch dotplot of two sequences

dreg Regular expression search of a nucleotide sequence

einverted Finds DNA inverted repeats

epestfind Finds PEST motifs as potential proteolytic cleavage sites

equicktandem Finds tandem repeats

est2genome Align EST and genomic DNA sequences

etandem Looks for tandem repeats in a nucleotide sequence

extractfeat Extract features from a sequence

extractseq Extract regions from a sequence

freak Residue/base frequency table or plot

fuzznuc Nucleic acid pattern search

fuzzpro Protein pattern search

fuzztran Protein pattern search after translation

garnier Predicts protein secondary structure

geecee Calculates fractional GC content of nucleic acid sequences

getorf Finds and extracts open reading frames (ORFs)

helixturnhelix Report nucleic acid binding motifs

hmoment Hydrophobic moment calculation

iep Calculates the isoelectric point of a protein

infoseq Displays some simple information about sequences

isochore Plots isochores in large DNA sequences

lindna Draws linear maps of DNA constructs

marscan Finds MAR/SAR sites in nucleic sequences

maskfeat Mask off features of a sequence

maskseq Mask off regions of a sequence

matcher Finds the best local alignments between two sequences

megamerger Merge two large overlapping nucleic acid sequences

merger Merge two overlapping nucleic acid sequences

msbar Mutate sequence beyond all recognition

needle Needleman-Wunsch global alignment

newcpgreport Report CpG rich areas

newcpgseek Reports CpG rich region

newseq Type in a short new sequence

noreturn Removes carriage return from ASCII files

notseq Exclude a set of sequences and write out the remaining ones

nthseq Writes one sequence from a multiple set of sequences

octanol Displays protein hydropathy

oddcomp Find protein sequence regions with a biased composition

palindrome Looks for inverted repeats in a nucleotide sequence

pasteseq Insert one sequence into another

patmatdb Search a protein sequence with a motif

pepcoil Predicts coiled coil regions

pepinfo Plots simple amino acid properties in parallel

pepnet Displays proteins as a helical net

pepstats Protein statistics

pepwheel Shows protein sequences as helices

pepwindow Displays protein hydropathy

pepwindowall Displays protein hydropathy of a set of sequences

plotcon Plot quality of conservation of a sequence alignment

plotorf Plot potential open reading frames

polydot Displays all-against-all dotplots of a set of sequences

preg Regular expression search of a protein sequence

prettyplot Displays aligned sequences, with colouring and boxing

prettyseq Output sequence with translated ranges

primersearch Searches DNA sequences for matches with primer pairs

revseq Reverse and complement a sequence

seqmatchall All-against-all comparison of a set of sequences

seqret Reads and writes sequences

showfeat Show features of a sequence

shuffleseq Shuffles a set of sequences maintaining composition

sigcleave Reports protein signal cleavage sites

sirna Finds siRNA duplexes in mRNA

sixpack Display a DNA sequence with 6-frame translation and ORFs

skipseq Reads and writes sequences, skipping first few

splitter Split a sequence into (overlapping) smaller sequences

supermatcher Match large sequences against one or more other sequences

syco Synonymous codon usage Gribskov statistic plot

tcode Fickett TESTCODE statistic to identify protein-coding DNA

textsearch Search sequence documentation. Slow, use SRS and Entrez!

tmap Displays membrane spanning regions

tranalign Align nucleic coding regions given the aligned proteins

transeq Translate nucleic acid sequences

trimest Trim poly-A tails off EST sequences

trimseq Trim ambiguous bits off the ends of sequences

twofeat Finds neighbouring pairs of features in sequences

union Reads sequence fragments and builds one sequence

vectorstrip Strips out DNA between a pair of vector sequences

water Smith-Waterman local alignment

wobble Wobble base plot

wordcount Counts words of a specified size in a DNA sequence

wordmatch Finds all exact matches of a given size between 2 sequences

Compute sequence length

Filter sequences by length

Concatenate FASTA alignment by species

FASTA-to-Tabular converts FASTA file to tabular format

Tabular-to-FASTA converts tabular file to FASTA format

Interpret ChIP-Seq Peaks Assist with interpretation of ChIP-Seq results

Manage workflows