Table 1 Characteristics of the available software to assign a phylogenetic label to the chromatogram fragment peaks

TAP-TRFLP

Web-based. Although it can be accessed through the older version of the Ribosomal Database Project, it has not been updated.

[10]

MiCA

Web-based. Newest version (MiCA 3) allows the selection of primers and in silico digestion of database sequences. Does not allow for user input sequences.

[11]

T-RFLP Phylogenetic Assignment Tool (PAT)

Web-based. Contains database of terminal restriction fragment sizes. Allows for the upload of fragment size database.

[12]

TReFID

Downloadable. Databases include 16S rRNA gene, dinitrogenase reductase gene (nifH) and nitrous oxide reductase gene (nosZ). Limited number of sequences although the user could expand it.

[13]

TRAMPR

R package. Based on a database of known T-RFLP profiles that can be constructed by the user. Loads data directly from ABI output files. Allows analysis with any type of gene, primer set and restriction enzyme.

[14]

ARB-software integrated tool (TRF-CUT)

Part of the ARB software. Allows for user input sequences that need to be aligned before analysis. Any type of gene could be analyzed.

[15]

TRiFLe

Java based. Allows for user input sequences. Can analyze any type of gene.

[16]

T-RFPred

Handles large database, such as 16S rRNA sequences from metagenomes, of user input clone sequences that do not need to be full length; multiple platforms. Makes use of the Ribosomal Database Project sequence database, which updates regularly. User needs to install Perl, Bioperl, BLAST and EMBOSS.

This study