Software

Percentile normalization (April 2018)

Sean Gibbons and Claire Duvallet
Correcting batch effects in microbiome case-control studies.
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dbotu3

WaveClust (Oct 2017)

Brian Cleary
OTU time series analysis by wavelet decomposition.
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waveclust

dbOTU3 (May 2017)

Scott Olesen
Calling ecologically-informed operational taxonomic units.
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dbotu3

TEXMEx (Mar 2015)

Scott Olesen
Visualizing microbial community dynamics.
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texmex

Latent strain analysis (Jan 2015)

Brian Cleary
Metagenomic read partitioning by latent factor analysis.
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LSA

Mystic (Sep 2014)

Scott Olesen and Sarah Preheim
Inferred biomass biogeochemical model of Mystic Lake.
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mystic

Distribution-based clustering (Sep 2014)

Sarah Preheim
Calling ecologically-informed operational taxonomic units.
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dbc

symsim 12/05/2012

Jesse Shapiro
Symsim is a simple simulation of sympatric speciation in recombining microbial populations. Read more...

symsim

STARRINIGHTS 12/12/2011

Jesse Shapiro
STARRInIGHTS is a computational pipeline for inferring homologous recombination breakpoints inpopulations of closely related bacterial genomes. Learn more...

starrnights

SparCC (July 2011)

Jonathan Friedman
Inference of correlations from 16S sequencing data.
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SparCC

SHE-RA 4/30/2010

Sonia Timberlake
SHE-RA is a tool that aligns the overlapping pair-end reads and generates composite long reads. The algorithm is applicable to any short read sequencing technology, and is open source. Read more... shera

ANGST 3/29/2009

Lawrence David
AnGST is a software package for the inference of prokaryotic gene family evolutionary histories.

Read more... angst

ADAPTML 5/1/2008

Lawrence David
AdaptML is a software package that will automatically partition groups of gene sequences...
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adaptml