SortMeRNA 2.1 – Filter rRNA Fragments from Metatranscriptomic data

SortMeRNA 2.1

:: DESCRIPTION

SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac / Linux
C++ Compiler

:: DOWNLOAD

SortMeRNA

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 15;28(24):3211-7. doi: 10.1093/bioinformatics/bts611.
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
Kopylova E, Noé L, Touzet H.

Metaxa2 2.2.3 – Identification and Classification of Small Subunit (SSU) rRNA Sequences

Metaxa2 2.2.3

:: DESCRIPTION

Metaxa2 is a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets

::DEVELOPER

The Bengtsson-Palme Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

Metaxa2

:: MORE INFORMATION

Citation:

Mol Ecol Resour. 2015 Mar 2. doi: 10.1111/1755-0998.12399.
metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data.
Bengtsson-Palme J1, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DG, Nilsson RH.

Antonie Van Leeuwenhoek. 2011 Oct;100(3):471-5. doi: 10.1007/s10482-011-9598-6. Epub 2011 Jun 15.
Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.
Bengtsson J, Eriksson KM, Hartmann M, Wang Z, Shenoy BD, Grelet GA, Abarenkov K, Petri A, Rosenblad MA, Nilsson RH.

rRNA phylogeny – Phylogenetic Analysis (using Phylip) of rRNA

rRNA phylogeny

:: DESCRIPTION

rRNA phylogeny is a program package to phylogenetic analyses (using Phylip) of rRNA using a matrix of empirical substitution rates and the OTRNA model.

4to20 translates DNA/RNA sequences to rRNA-coded sequences in 20-letter code
20to4 translates rRNA-coded sequences to 4-letter code
nadist performs Distance analysis using the OTRNA model and gamma-distributed rates.
rRNAdist, rRNAml, rnaml: modified versions of protdist, protml, protmlk from PHYLIP to use the rRNA matrices.
etseqgen: modification of PSeq-gen to use the PMB model or the Bacterial SSU rRNA model.

::DEVELOPER

The Tillier Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux

:: DOWNLOAD

rRNA phylogeny

:: MORE INFORMATION

Citation:

Empirical substitution models for Ribosomal RNA
Andrew Smith, Thomas W. H. Lui and Elisabeth R. M. Tillier,
Mol Biol Evol (2004) 21: 419-427

High apparent rate of simultaneous compensatory base-pair substitutions in ribosomal RNA
Tillier, E. R. M. and R. A. Collins,
Genetics (1998) 148: 1993-2002