Supporting information 2
List of computational tools for single layer analysis
Tool name
Genetic constraints
ACUA
E-CAI
MosaicFinder
OperonDB
RegulonDB
ProOpDB
DOOR
FusionFinder
CAIAP
Genomic constraints
GC-Profile
GraphDNA
IslandViewer
MobilomeFinder
PIPS
PAIDB
Taxonomic information
CGAT
MicrobesOnline
Beast
Microscope
MEGA software
Sybil
VISTA
EDGAR
Metabolic information
RAST/Model Seed
MicrobesFlux
FAME
Pathway Tools Software
COPABI
CARMEN
Kbase
GEMSiRV
RAVEN
COVAIN
Metabolomics
MBRole
MetPA
Website
http://www.bioinsilico.com/acua
http://genomes.urv.es/CAIcal/E-CAI/
http://sourceforge.net/projects/mosaicfinder/
http://operondb.cbcb.umd.edu/cgi-bin/operondb/operons.cgi
http://regulondb.ccg.unam.mx/
http://operons.ibt.unam.mx/OperonPredictor/
http://csbl1.bmb.uga.edu/OperonDB/
http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/
http://www.unifi.it/scibio/bioinfo/caiap/html/
http://tubic.tju.edu.cn/GC-Profile/
http://athena.bioc.uvic.ca/virology-ca-tools/graphdna/
http://www.pathogenomics.sfu.ca/islandviewer
http://db-mml.sjtu.edu.cn/MobilomeFINDER/online.htm
http://www.genoma.ufpa.br/lgcm/pips/
https://www.gem.re.kr/paidb/about_paidb.php
http://mbgd.genome.ad.jp/CGAT/
http://www.microbesonline.org/
http://beast.bio.ed.ac.uk/Main_Page
http://www.cns.fr/agc/microscope/home/index.php
http://www.megasoftware.net/
http://sybil.sourceforge.net/
http://genome.lbl.gov/vista/index.shtml
http://edgar.cebitec.uni-bielefeld.de/cgi-bin/edgar_login.cgi
http://rast.nmpdr.org/, http://www.theseed.org/
http://tanglab.engineering.wustl.edu/static/MicrobesFlux.html
http://f-a-m-e.org/
http://bioinformatics.ai.sri.com/ptools/
http://carmen.cebitec.uni-bielefeld.de
www.kbase.us
http://sb.nhri.org.tw/GEMSiRV/en/GEMSiRV
http://www.sysbio.se/BioMet
http://www.univie.ac.at/mosys/software.html
http://csbg.cnb.csic.es/mbrole/
http://metpa.metabolomics.ca/MetPA/faces/Home.jsp
Reference
(1)
(2)
(3)
(4)
(5)
(6)
(7)
(8)
(9)
(10)
(11)
(12)
(13)
(14)
(15)
(16)
(17)
(18)
(19)
(20)
(21)
(22)
(23)
(24-26)
(27)
(28)
(29, 30)
(31)
(32)
(33)
(34)
(35)
(36)
(37)
MSEA
MAVEN
metaP
metatt
Transcriptomics
Bioconductor
RobiNA
Mayday
CPTRA
BASE
EMMA 2
ExpressionPlot
MIMAS 3.0
Epigenomics
RESID db
SMRT Analysis
FindMod
FindPept
PeptideMass
Proteomics
DIP db
STRING db
Mascot
MFPaQ
Compid
Phenomics
DuctApe
PhD database
RetroSpect
PheMaDB
Single cell microscopy
Tri-track
RELION
CellC
Ecosystem information
MG-RAST
FANTOM
MEGAN
Camera
IMG
http://www.msea.ca.
http://genomics-pubs.princeton.edu/mzroll/index.php
http://metabolomics.helmholtz-muenchen.de/metap2/
http://metatt.metabolomics.ca/MetATT/
http://www.bioconductor.org/
http://mapman.gabipd.org/web/guest/robin
http://www-ps.informatik.uni-tuebingen.de/mayday/wp/
http://people.tamu.edu/~syuan/cptra/
http://base.thep.lu.se/
http://www.cebitec.uni-bielefeld.de/comics/index.php/comics-software
www.expressionplot.com/
http://multiomics.sourceforge.net/
http://pir.georgetown.edu/resid/
https://github.com/PacificBiosciences/SMRT-Analysis
http://web.expasy.org/findmod/
http://web.expasy.org/findpept/
http://web.expasy.org/peptide_mass/
http://dip.doe-mbi.ucla.edu/dip/Main.cgi
http://string-db.org/
https://www.msi.umn.edu/sw/mascot
http://mfpaq.sourceforge.net/
http://users.utu.fi/lanatr/compid
http://combogenomics.github.io/DuctApe/
http://apps.sbri.org/gpdb
http://www.biolog.com/
http://binf.gmu.edu/wchang3/phemadb/pheno/
http://www2.mrc-lmb.cam.ac.uk/groups/scheres/software.html
https://sites.google.com/site/cellcsoftware/
http://metagenomics.anl.gov/
http://www.sysbio.se/Fantom/
http://ab.inf.uni-tuebingen.de/software/megan/
http://camera.calit2.net/
http://img.jgi.doe.gov/
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