ProtTest v3.2

ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT). At the same time, ProtTest obtains model-averaged estimates of different parameters (including a model-averaged phylogenetic tree) and calculates their importance(Posada and Buckley 2004). ProtTest differs from its nucleotide analog jModeltest (Posada 2008) in that it does not include likelihood ratio tests, as not all models included in ProtTest are nested.

Accessing the software

To load the module:

$ module load apps/prottest3/v3.2

An example command to include in your job script:

java -jar ${PROTTEST_JAR} -i COX2_PF0016/alignment -all-matrices -all-distributions -threads ${SLURM_NTASKS}

The module command sets the environment variable PROTTEST_EXAMPLES too which is a directory with some sample programs in it.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

  • ProtTest cannot be run as a parallel job across nodes on this service; it can utilise multiple cores on a node.

Other Information

The Support Level for this application is An.

Visit the ProtTest website for more information regarding this application.

Last modified: 7 December 2017