Skip to main content

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

From: T-RFPred: a nucleotide sequence size prediction tool for microbial community description based on terminal-restriction fragment length polymorphism chromatograms

Software package Characteristics Reference
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
  1. Complete sequence at least at the 5'-end of the sample sequence is needed in every case except for T-RFPred, as this program finds the closest related sequence in the Ribosomal Database Project database by BLASTN.