63
Sample
no.
Name
Weblink
References
9.
MetaPhyler
http://metaphyler.cbcb.umd.edu
Liu et al. (2011)
10.
MTR
http://cs.ru.nl/gori/software/MTR.tar.gz
Gori et al. (2011)
11.
NBC
http://nbc.ece.drexel.edu
Rosen et al. (2011)
12.
PaPaRa
http://www.exelixislab.org/software.html
Berger and Stamatakis (2011)
13.
PhyloPythia
–
Patil et al. (2012)
14.
Phymm
–
Brady and Salzberg (2011)
15.
RAIphy
–
Nalbantoglu et al. (2011)
16.
SOrt-ITEMS
http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS
Monzoorul Haque et al. (2009)
17.
SPHINX
http://metagenomics.atc.tcs.com/SPHINX/
Mohammed et al. (2011)
18.
TACOA
–
Diaz et al. (2009)
19.
Treephyler
http://www.gobics.de/fabian/treephyler.php
Schreiber et al. (2010)
Tools for functional profiling
1.
HUMAnN
–
Abubucker et al. (2012)
2.
metaSHARK
http://bioinformatics.leeds.ac.uk/shark/
Hyland et al. (2006)
3.
Predicted Relative Metabolic Turnover
(PRMT)
–
Larsen et al. (2011)
4.
RAMMCAP
http://tools.camera.calit2.net/camera/rammcap/
Li (2009)
Tools for interaction networks
1.
SparCC
https://bitbucket.org/yonatanf/sparcc
Friedman and Alm (2012)
2.
CCREPE
–
Faust et al. (2012)
Tools for statistical tests
1.
Metastats
–
Paulson et al. (2011)
2.
LefSe
http://huttenhower.sph.harvard.edu/lefse/
Segata et al. (2011)
3.
ShotgunFunctionalizeR
http://shotgun.zool.gu.se
Kristiansson et al. (2009)
(continued)
6.1 Tools for Assembly and Annotation