Search Google Appliance


Biology/Genetics Software

This page provides a list of biology/genetics software that the ARC offers to users.

Name Description Hosted Server

ABySS

A de novo, parallel, paired-end sequence assembler

gravel.research.pdx.edu

AllpathsLG

Sequencing Tool

research.pdx.edu

ARB

Biological Sequence tool for UNIX

research.pdx.edu

Biom_format-0.9.3

Bioinformatics File Reader

research.pdx.edu

BioPerl

Perl tools for bioInformatics, genomics, and Life Science research.

research.pdx.edu

Consed

Viewing, Editing, and Finishing DNA Sequence Assemblies

research.pdx.edu

EMBOSS

Molecular Biology Suite

gravel.research.pdx.edu

FASTA

Bioinformatics

gravel.research.pdx.edu

Fasttree-2.1.4

Infers Approximently-Maxium-Likelihood Phylogenetic Tree from Alignments of Nucleotide or Protein Sequences

esearch.pdx.edu

Gmap

Bio-sequence analysis

gravel.pdx.edu

Glimmer

Gene Locator and Interpolated Markov Modeler

gravel.pdx.edu

Greengenes

162S rRNA Gene Sequencer

research.pdx.edu

Khmer

K-mer Based Dataset Analysis and Transformations (Assembly of metagenomes and mRNA)

research.pdx.edu

MEGAN-4.67.2

Meta Gnome Analyizer

research.pdx.edu

Meta-velvetg 1.2.02

Genetics Software

research.pdx.edu

MrBayes

Bayesian inference of phylogeny

gravel.research.pdx.edu

MPIBLAST

Biomedical and Genomic

gravel.research.pdx.edu

NCBI

Biomedical and Genomic

gravel.research.pdx.edu

PyCogent-1.5.1

Gemonic Library for Python

research.pdx.edu

PhyML-3.0

Phylogenetic Maxium Likelihood

research.pdx.edu

Pynast-1.1

16S rDNA Sequence Library for Python

research.pdx.edu

Qiime-1.5.0

Comparsion and Analysis of Microbial Communities

research.pdx.edu

Rtax-0.981

Rapid Taxonomic Assignments of Paired-end Reads

research.pdx.edu

Screed

Biological Sequence Library for Python

research.pdx.edu

uclust-1.2.22

Exterme High-speed Sequence Clustering, Aligment and Database Search

research.pdx.edu

usearch-5.2.32

Molecular Biology Suite

research.pdx.edu

Velvet

Genetics Software

research.pdx.edu

Further Resources

For more information on research computing software, contact Academic & Research Computing.

You can also contact the Helpdesk for additional assistance.