Applied Microbial Bioinfomatics - Links

Programs and Databases

1. Sequin: Submission of sequences in GenBank*

http://www.ncbi.nlm.nih.gov/Sequin/

2. Alignments:

Muscle: faster alignments and it can be install in your computer if you have more than 500 sequences*

http://www.ebi.ac.uk/Tools/muscle/

ClustalW: commonly used.

http://www.ebi.ac.uk/Tools/clustalw2/index.html

3. Alignment Editors:

Mega*

http://www.megasoftware.net/

Jalview:

http://www.jalview.org/*

Bioedit:

http://www.mbio.ncsu.edu/BioEdit/page2.html*

GeneDoc:

http://www.nrbsc.org/gfx/genedoc/

4.Fungal Databases:

UNITE*:

http://unite.ut.ee/

Fungal Metagenomes-Taylor's Lab -University of Alaska:

http://www.borealfungi.uaf.edu/

Index Fungorum*:

http://www.indexfungorum.org/

Rytas Vilgalys Lab*:

http://www.biology.duke.edu/fungi/mycolab/primers.htm

Tom Brun’s Lab:

http://mollie.berkeley.edu/~bruns/

Fungal Tree of Life*:

http://aftol.org/

Database of PCR Primers for Phytopathogenic Fungi*

http://www.sppadbase.com/

CYBERLIBER*

http://www.cybertruffle.org.uk/cyberliber/

CBS

http://www.cbs.knaw.nl/

Mycobank*

http://www.mycobank.org/

Myconet

http://www.fieldmuseum.org/myconet/

Tom Volk Website

Tom Volk's Fungi Collection

Fungi Online

Barcode of Life

http://www.barcoding.si.edu/

Biodiversity Institute of Ontario

http://www.biodiversity.uoguelph.ca/

CBS-KNAW fungal biodiversity centre

http://www.cbs.knaw.nl/

Qbol

http://www.pri.wur.nl/UK/research/projects/qbol

European Consortium for the Barcode of Life

http://www.ecbol.org/

Barcode of Life Data Systems

http://www.boldsystems.org/views/login.php

Fusarium ID

http://isolate.fusariumdb.org/

5. Bacterial Databases:

GreenGenes*:

http://greengenes.lbl.gov/cgi-bin/nph-index.cgi

Ribosomal Database Project*:

http://rdp.cme.msu.edu/

ARB:

http://www.arb-home.de/

probeBase

http://www.microbial-ecology.net/probebase/list.asp?list=probes

BioinformaticsToolKit

http://www.bioinformatics-toolkit.org/

6. Plant Databases:

http://www.phytozome.net/*

7. Metagenomes and Microbial Genomes:

Fungal Genum-The hyphal tip

http://fungalgenomes.org/blog/

JGI:

http://www.jgi.doe.gov/

Broad Institute:

http://www.broadinstitute.org/science/projects/fungal-genome-initiative/fungal-genome-initiative

IMG:

http://img.jgi.doe.gov/cgi-bin/pub/main.cgi*

VISTA:

http://genome.lbl.gov/vista/index.shtml

Genomes OnLine Database

MEGAN*

http://www-ab.informatik.uni-tuebingen.de/software/megan

CAMERA

http://camera.calit2.net/about/

SCATA

http://scata.mykopat.slu.se/

Phylosity

http://www.bioportal.uio.no/appinfo/show.php?app=phylosity

Lee Taylor

https://biotech.inbre.alaska.edu/fungal_portal/

EupathDB: Eukaryotic Pathogen Database Resources

http://eupathdb.org/eupathdb/

Fungal Genomics Program

http://genome.jgi-psf.org/programs/fungi/index.jsf

Galaxy

http://main.g2.bx.psu.edu/

MG-RAST

http://metagenomics.nmpdr.org/

Terragenome

http://www.terragenome.org/

GOLD

http://www.genomesonline.org/

8. Diversity Estimators and Community Analysis Programs:

Qiime: 

http://qiime.org/

MOTHUR:

http://schloss.micro.umass.edu/wiki/Main_Page

UNIFrac:

http://bmf2.colorado.edu/unifrac/index.psp

http://bmf2.colorado.edu/fastunifrac/index.psp

9. Primer Design

Primer3:

http://frodo.wi.mit.edu/primer3/

OligoAnalyzer*

http://www.idtdna.com/analyzer/applications/oligoanalyzer/Default.aspx

10. Sequencing:

Animation of Sanger sequencing*

454 Sequencing*

Illumina sequencing technology

http://www.illumina.com/technology/sequencing_technology.ilmn

Helicos: Single-Molecule DNA sequencing

http://link.brightcove.com/services/player/bcpid1827871101?bctid=1618618549

11. Editing Chromatograms

FinchTv

http://www.geospiza.com/Products/finchtv.shtml

Phred/Phrap

http://www.phrap.org/

12. Other Technologies

RNAi

http://www.pbs.org/wgbh/nova/sciencenow/3210/02.html

13. Phylogenetic Analysis

http://www.phylo.org/links/

Tree of Life Projects*

http://www.phylo.org/atol/

TreeBase

http://www.treebase.org/treebase-web/home.html

NESCent*

http://www.nescent.org/index.php

Phylip

http://evolution.genetics.washington.edu/phylip.html

PAUP

http://paup.csit.fsu.edu/

MrBayes

http://mrbayes.csit.fsu.edu/

14. Societies

APSnet

http://www.apsnet.org/

ASM

http://www.asm.org/index.php

MSA

http://www.msafungi.org/

ESA

http://www.esa.org/

IMS

http://www.ima-mycology.org/index.html

15. Primers

Bacteria

http://www.lutzonilab.net/primers/page604.shtml

Fungi

http://biology.duke.edu/fungi/mycolab/primers.htm

15. Free Books:

http://books.nap.edu/catalog.php?record_id=11902

16.Research Networks:

PAFNET: Plant-associated fungal network

FESIN: Fungal Environmental Sampling and Informatics Network

AFTOL: Assembling the Fungal Tree of Life

Medical Mycology

CDC Mold

http://www.cdc.gov/mold/links.htm

PRACTICE FILES