NAME

       prottest - Selection of best-fit models of protein evolution (sequential version)

SYNOPSIS

       prottest -i alignm_file [OPTIONS]

DESCRIPTION

        PROTTEST (ModelTest's relative) is a program for selecting the model of
        protein evolution that best fits a given set of sequences (alignment).
        This java program is based on the Phyml program (for maximum likelihood
        calculations and optimization of parameters) and uses the PAL library as
        well. Models included are empirical substitution matrices (such as WAG,
        LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam,
        MtArt, HIVb, and HIVw) that indicate relative rates of amino acid
        replacement, and specific improvements (+I:invariable sites, +G: rate
        heterogeneity among sites, +F: observed amino acid frequencies) to
        account for the evolutionary constraints impossed by conservation of
        protein structure and function. ProtTest uses the Akaike Information
        Criterion (AIC) and other statistics (AICc and BIC) to find which of the
        candidate models best fits the data at hand.

OPTIONS

       -i alignment_filename

              Alignment input file (required)

       -t tree_filename

              Tree file (optional) [default: NJ tree]

       -o output_filename

              Output file (optional) [default: standard output]

       -log enabled/disabled

              Enables / Disables PhyML logging into log directory (see prottest.properties)

       -[matrix]

              Include  matrix  (Amino-acid)  =  JTT  LG DCMut MtREV MtMam MtArt Dayhoff WAG RtREV
              CpREV Blosum62 VT HIVb HIVw FLU

              If you don't specify any matrix, all matrices displayed above will be included.

       -I

              Include models with a proportion of invariable sites

       -G

              Include models with rate variation among sites and number of categories

       -IG

              include models with both +I and +G properties

       -all-distributions

              Include models with rate variation among sites, number of categories and both

       -ncat number_of_categories

              Define number of categories for +G and +I+G models [default: 4]

       -F

              Include models with empirical frequency estimation

       -AIC

              Display models sorted by Akaike Information Criterion (AIC)

       -BIC

              Display models sorted by Bayesian Information Criterion (BIC)

       -AICC

              Display models sorted by Corrected Akaike Information Criterion (AICc)

       -DT

              Display models sorted by Decision Theory Criterion

       -all

              Displays a 7-framework comparison table

       -S optimization_strategy

              Optimization strategy mode: [default: 0]

              0: Fixed BIONJ JTT

              1: BIONJ Tree

              2: Maximum Likelihood tree

              3: User defined topology

       -s moves

              Tree search operation for ML search: NNI (fastest), SPR (slowest),  BEST  (best  of
              NNI and SPR) [default: NNI]

       -t1

              Display best-model's newick tree [default: false]

       -t2

              Display best-model's ASCII tree [default: false]

       -tc consensus_threshold

              Display  consensus  tree  with  the specified threshold, between 0.5 and 1.0 [0.5 =
              majority rule consensus ; 1.0 = strict consensus]

       -threads number_or_threads

              Number of threads requested to compute (only if MPJ is not used) [default: 1]

       -verbose

              Verbose mode [default: false]

EXAMPLE

       prottest -i alignm_file -t tree_file -S 0 -all-distributions -F -AIC -BIC -tc 0.5 > output