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Start Your TrialStatAlign is an extendable software package for Bayesian analysis of protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable quantification of the uncertainty in these estimates..
The interface is selected with tool=STATALIGN_ACCESS
Supported parameters:
Input files
input.seqfile1_ - Primary Input File (First gene to analyze)
input.seqfile2_ - Specify a second input file (Secon gene to analyze)
input.seqfile3_ - Specify a third input file (Third gene to analyze)
input.seqfile4_ - Specify a fourth input file ((Fourth gene to analyze)
input.treefile_ - Specify a tree
Visible Parameters
vparam.runtime_ - (Float) maximum number of hours to run (default=0.5)
vparam.more_memory_ - (Switch) - I need more memory (default=0).
vparam.num_chains_ - (Switch) - Specify 1 to give a run with two chains (default=0).
vparam.specify_specify_treeuse_ - (Excl) - How shall the selected tree be used? I: used as initial tree, sampled during MCMC; T: the topology is fixed throughout the MCMC analysis, edges are sampled; E: both topology and edge lengths are fixed during the MCMC
vparam.specify_model_ - (Excl) Choose the substitution model: Jones, Kimura3 (Default for DNA), RtREV; MtMam; Tamura92; JukesCantor; Dayhoff (Default for proteins); Wag; TamuraNei; Felsenstein84; Blosum; CpRev; Vt; MtREV; ReversibleNucleotide; Felsenstein81; HKY85
vparam.specify_burnin_ - String - number of burnin steps, where k=10^3 and m=10^6; default 20k.
vparam.specify_cycles_ - String - number of steps, where k=10^3 and m=10^6; default 50k.
vparam.specify_rate_ - Integer - rate; default 100.
vparam.specify_randomisationperiod_ - Integer - randomization period; no default, optonal.
vparam.automate_burn_ - Switch - automate the burnin. default = 0
vparam.automate_cycle_ - Switch - automate the cycle. default = 0
vparam.automate_rate_ - Switch - automate the rate. default = 0
vparam.specify_seedval_ - Integer - specify a seed; default = 1
vparam.report_burnin_ - Switch - Report the burnin. default = 0
vparam.specify_output - Excl - Fasta, StatAlign, Clustal, Phylip, Nexus; default =Fasta.