This is the command prottest that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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