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*
Jalview:
Bioedit:
http://www.mbio.ncsu.edu/BioEdit/page2.html*
GeneDoc:
http://www.nrbsc.org/gfx/genedoc/
4.Fungal Databases:
UNITE*:
Fungal Metagenomes-Taylor's Lab -University of Alaska:
http://www.borealfungi.uaf.edu/
Index Fungorum*:
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*:
Database of PCR Primers for Phytopathogenic Fungi*
CYBERLIBER*
http://www.cybertruffle.org.uk/cyberliber/
CBS
Mycobank*
Myconet
http://www.fieldmuseum.org/myconet/
Tom Volk Website
Barcode of Life
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
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*:
ARB:
probeBase
http://www.microbial-ecology.net/probebase/list.asp?list=probes
BioinformaticsToolKit
http://www.bioinformatics-toolkit.org/
6. Plant Databases:
7. Metagenomes and Microbial Genomes:
Fungal Genum-The hyphal tip
http://fungalgenomes.org/blog/
JGI:
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
MEGAN*
http://www-ab.informatik.uni-tuebingen.de/software/megan
CAMERA
http://camera.calit2.net/about/
SCATA
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
Fungal Genomics Program
http://genome.jgi-psf.org/programs/fungi/index.jsf
Galaxy
MG-RAST
http://metagenomics.nmpdr.org/
Terragenome
GOLD
8. Diversity Estimators and Community Analysis Programs:
Qiime:
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*
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
12. Other Technologies
RNAi
http://www.pbs.org/wgbh/nova/sciencenow/3210/02.html
13. Phylogenetic Analysis
Tree of Life Projects*
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
MrBayes
14. Societies
APSnet
ASM
MSA
ESA
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