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Tool Listing

The following tool listing briefly describes the available tools on the application server. Collaborators are able to remotely run these tools from the application server for their projects. For more information on a specific tool, please click on the tool name to an external link. To request access to the application server, please email tg-help@ucdavis.edu.

Tool NameVersionDescription
biojava 3.0.1
BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures.
bioperl 1.6.901
Bioperl is a collection of perl libraries that ease common bioinformatic needs and integrate with common file formats.
biopython 1.5.7
Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
bowtie 0.12.7
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
bwa 0.5.9
Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW.
cap3 (2007) CAP 3 is a contig assembly program that can take in FASTA formatted sequences and quality scores
cd-hit 4.5.5
CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset.
Celera Assembler 6.1
Celera Assembler is scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. Celera Assembler has enabled many advances in genomics, including the first whole genome shotgun sequence of a multi-cellular organism (Myers 2000) and the first diploid sequence of an individual human (Levy 2007). Celera Assembler was developed at Celera Genomics starting in 1999. It was released to SourceForge in 2004 as the wgs-assembler under the GNU General Public License. The pipeline revised for 454 data was named CABOG (Miller 2008).
clustalw2 2.1
ClustalW is a multiple alignment utility for DNA and protein sequences
consed 20.0
Consed is a graphical interface for editing phrap output.
dnaSAM 20100621
DNA Sequence Analysis and Manipulation (DnaSAM), addresses the challenges of data manipulation, summary statistic estimation and statistical hypothesis testing for large-scale resequencing projects. The program is capable of performing a large number of standard and newly designed tests of neutrality for multiple sequence alignments of resequenced gene loci. In addition, the program allows hypothesis testing using complex and user-specified null models.
eagleview 2.0 EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations.
emboss 6.3.1
EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. EMBOSS integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
exonerate 2.2.0
Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.
fasta36 36.3.5
The FASTA packages contains many programs for searching DNA and protein databases and for evaluating statistical significance from randomly shuffled sequences.
FASTX-Toolkit 0.0.13
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
freebayes 0.8.4
FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.
GSL 1.15
The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
InterProScan 4.8
InterPro is a collaborative project aimed at providing an integrated layer on top of the most commonly used signature databases by creating a unique, non- redundant characterisation of a given protein family, domain or functional site. The InterPro database integrates PROSITE, PRINTS, Pfam, ProDom, SMART, TIGRFAMs, PIR superfamily, SUPERFAMILY, Gene3D, PANTHER and HAMAP databases.
Lagan 2.0
The Lagan Tookit is a set of alignment programs for comparative genomics.
libsequence 1.7.3
libsequence is a C++ library designed to aid writing applications for genomics and evolutionary genetics. A large amount of the library is dedicated to the analysis of "single nucleotide polymorphism", or SNP data.
libsequence-analysis 0.8.0
C++ software for evolutionary genetic analysis built off the libsequence library.
The mira genome fragment assembler is a specialised assembler for sequencing projects classified as 'hard' due to high number of similar repeats. For EST transcripts, miraEST is specialised on reconstructing pristine mRNA transcripts while detecting and classifying single nucleotide polymorphisms (SNP) occuring in different variations thereof. The assembly system is using iterative multipass strategies centered on usage of high confidence regions within sequences and has a fallback strategy for using low confidence regions when needed.
Muscle 3.8.31
MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two.
NCBI Blast 2.2.25
TreeGenes has installed and maintains a local version of the WWW-BLAST server called Local BLAST with databases which are updated weekly. Having a local server offers improved performance and security and allows us to create our own BLAST DBs.
NCBI C++ Toolkit 7.0.0
The toolkit is used internally at NCBI to process and analyze data from a variety of sources to build and maintain the unified databases and also serves as the components for the end-user applications NCBI distributes.
NCBI Genome Workbench 2.3.2
NCBI Genome Workbench is an integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at NCBI, and mix this data with your own private data.
Oases 0.1.21
Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
Phase 2.0 PHASE is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.
phrap 1.090518
Phrap ("phragment assembly program", or "phil's revised assembly program") is a program for assembling shotgun DNA sequence data.
phred 0.071220.c
Phred reads DNA sequencer trace data, calls bases, assigns quality values to the bases, and writes the base calls and quality values to output files.
phylip 3.69 A package of tools: PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).
polybayes 3.0
PolyBayes is a computer program for the automated analysis of single-nucleotide polymorphism (SNP) discovery in redundant DNA sequences.
polyphred 6.18
PolyPhred identifies substitution SNPs as potential heterozygotes by comparing traces in a sequence assembly.
primer3 2.2.3
Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction").
probconsRNA 1.12
PROBCONS is a novel tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date.
R 2.13.0
R is a language and environment for statistical computing and graphics.
readseq (2010) Reads and writes nucleic/protein sequences in various formats. Data files may have multiple sequences.
RECON 1.05
The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences.
repeatmasker 3.3.0
Screens DNA sequences for interspersed repeats and low complexity DNA sequences.
rmblast 1.2 RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.
samtools 0.1.17 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Selenoprofiles 2.2d
Selenoprofiles can be used to search for any protein family (also non-selenoprotein), given an input profile alignment. This pipeline combines standard gene prediction tools to provide a clean and fast way to scan genomes for protein families, and provides a wide repertoire of output formats which can also be extended by the user.
SeqTools 4.10
A suite of tools for visualising sequence alignments.
sequin 11.0
Sequin is a program designed to aid in the submission of sequences to the GenBank, EMBL, and DDBJ sequence databases.
sim4 Sim4 is a similarity-based tool for aligning an expressed DNA sequence (EST, cDNA, mRNA) with a genomic sequence for the gene.
structure 2.3.3
Structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers.
Trans-ABYSS 1.2.0
Trans-ABySS is a software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data. The pipeline accepts assemblies that were generated across a wide range of k values in order to address variable transcript expression levels.
Trinity r2011-11-26
Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data.
twinscan 3.5 predicting gene structure
uclust 3.0
This program implements the USEARCH, UCLUST, UHIRE and UCHIME algorithms for database search, clustering and chimeric sequence detection respectively.
usearch 5.1.221
USEARCH is a unique high-throughput sequence analysis tool. It is a distributed as single binary program that implements a suite of algorithms.
velvet 1.1.04
Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454.
wise2 2.2.0
Wise2 is a package focused on comparisons of DNA sequence and protein sequence.

Icon 03 Updates

Walnut genome project releases assembly (v1.0) of the Juglans regia genome PineRefSeq project releases assembly (v0.5) of the Pseudotsuga menziesii genome PineRefSeq project releases assembly (v1.0) of the Pinus lambertiana genome CartograTree (v3.0), a map interface that works with DiversiTree to bring together genomics, ecological, and trait data is now live! PineRefSeq project releases assembly (v1.01) of the Pinus teada genome SMarTForests Project releases the third assembly of the Picea glauca genome

Icon 01 Events

ProCoGen Final Open Conference and Workshops: Promoting Conifer Genomic Resources

Orléans, France
November 30 - December 4, 2015
Plant and Animal Genome Conference

San Diego, CA, USA
January 9, 2015 - January 13, 2016
Forest Genetics for Productivity Conference: The Next Generation

Rotorua, New Zealand
March 14-18, 2016