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Tools
Get Data
cd-hit
Cluster or compare biological sequence datasets
Upload File
from your computer
UCSC Main
table browser
UCSC Test
table browser
UCSC Archaea
table browser
EBI SRA
ENA SRA
Get Microbial Data
BioMart
Ensembl server
CBI Rice Mart
rice mart
GrameneMart
Central server
modENCODE fly
server
Flymine test
server
Flymine
server
modENCODE modMine
server
MouseMine
server
Ratmine
server
metabolicMine
server
YeastMine
server
modENCODE worm
server
Wormbase
test server
WormBase
server
ZebrafishMine
server
EuPathDB
server
HbVar
Human Hemoglobin Variants and Thalassemias
Collection Operations
Unzip Collection
Zip Collection
Filter failed
datasets from a collection
Flatten Collection
into a flat list of datasets
Merge Collections
into single list of datasets
Relabel List Identifiers
from contents of a file
Filter List
from contents of a file
Sort Collection
of list of datasets
Lift-Over
Convert genome coordinates
between assemblies and genomes
Text Manipulation
Add column
to an existing dataset
Concatenate datasets
tail-to-head
Cut
columns from a table
Merge Columns
together
Convert
delimiters to TAB
Create single interval
as a new dataset
Change Case
of selected columns
Paste
two files side by side
Remove beginning
of a file
Select random lines
from a file
Select first
lines from a dataset
Select last
lines from a dataset
Trim
leading or trailing characters
Line/Word/Character count
of a dataset
Secure Hash / Message Digest
on a dataset
Convert Formats
AXT to concatenated FASTA
Converts an AXT formatted file to a concatenated FASTA alignment
AXT to FASTA
Converts an AXT formatted file to FASTA format
AXT to LAV
Converts an AXT formatted file to LAV format
BED-to-GFF
converter
GFF-to-BED
converter
LAV to BED
Converts a LAV formatted file to BED format
MAF to BED
Converts a MAF formatted file to the BED format
MAF to Interval
Converts a MAF formatted file to the Interval format
MAF to FASTA
Converts a MAF formatted file to FASTA format
Wiggle-to-Interval
converter
SFF converter
GTF-to-BEDGraph
converter
Wig/BedGraph-to-bigWig
converter
BED-to-bigBed
converter
Filter and Sort
Filter
data on any column using simple expressions
Sort
data in ascending or descending order
Select
lines that match an expression
GFF
Extract features
from GFF data
Filter GFF data by attribute
using simple expressions
Filter GFF data by feature count
using simple expressions
Filter GTF data by attribute values_list
Join, Subtract and Group
Join two Datasets
side by side on a specified field
Compare two Datasets
to find common or distinct rows
Group
data by a column and perform aggregate operation on other columns.
Extract Features
Gene BED To Exon/Intron/Codon BED
expander
Fetch Sequences
Extract Genomic DNA
using coordinates from assembled/unassembled genomes
Fetch Alignments
Extract Pairwise MAF blocks
given a set of genomic intervals
Extract MAF blocks
given a set of genomic intervals
Split MAF blocks
by Species
Stitch MAF blocks
given a set of genomic intervals
Stitch Gene blocks
given a set of coding exon intervals
MAF Coverage Stats
Alignment coverage information
Join MAF blocks
by Species
Filter MAF blocks
by Species
Filter MAF blocks
by Size
Extract MAF by block number
given a set of block numbers and a MAF file
Reverse Complement
a MAF file
Filter MAF
by specified attributes
SpCLUST
SpCLUST-EDNAFULL
Takes a FASTA file as input and gives back the gnomes grouping using EDNAFULL
SpCLUST-EDNAFULL Fast
Takes a FASTA file as input and gives back the gnomes grouping using fast alignment and EDNAFULL
SpCLUST-BLOSUM62
Takes a FASTA file as input and gives back the gnomes grouping using BLOSUM62
SpCLUST-BLOSUM62 Fast
Takes a FASTA file as input and gives back the gnomes grouping using fast alignment and BLOSUM62
SpCLUST-PAM250
Takes a FASTA file as input and gives back the gnomes grouping using PAM250
SpCLUST-PAM250 Fast
Takes a FASTA file as input and gives back the gnomes grouping using fast alignment and PAM250
SpCLUST-V3
SpCLUST-V3
Biological sequences clustering using GMM
SpCLUST-V2
SpCLUST-V2
Biological sequences clustering using GMM
Statistics
Summary Statistics
for any numerical column
Count
occurrences of each record
Graph/Display Data
Bar chart
for multiple columns
Boxplot
of quality statistics
VCF to MAF Custom Track
for display at UCSC
Workflows
All workflows
History
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