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GARLI - Genetic Algorithm for Rapid Likelihood Inference

Version 2.0 - Author(s): Derrick J. Zwickl (zwickl@ku.edu) - Category: Phylogenetics

General Settings

Analysis type * :
ML searchBootstrap

Number of replicates (1 - 2000) * :

* Sequence data file :

Starting tree (if supplying one, select 'Upload' and choose file below) :
RandomStepwiseUpload

Starting tree file :

Attachment branches evaluated for each taxon (minimum 1) :

Outgroup taxa numbers (separated by spaces) :

Constraint file :

Perform initial rough optimization

Output site likelihoods

Collapse zero-length branches into polytomies

Write trees to file in Phylip format as well as Nexus format

Model Parameters

Perform partitioned analysis

Non-partitioned Analysis

Model type :
NucleotideAmino acidCodon-Amino acidCodon

Nucleotide

Rate matrix :
All rates equal (1rate)HKY (2rate)General time-reversible (6rate)Fixed

Base frequencies :
EqualEmpiricalEstimateFixed

Proportion of invariant sites :
NoneEstimateFixed

Rate heterogeneity model :
Equal rate for all sites (none)Gamma distribution (gamma)

Number of rate categories (1 to 20) :

Population

Selection intensity (0.01 to 5.0) :

Number of individuals (2 to 100) :

Branch-length Optimization

Starting precision (0.005 - 5.0) :

Minimum precision (0.001 - 0.01) :

Tree rejection threshold (0 to 500) :

Number of precision reductions (0 - 100) :

Mutation

Model parameter mutation weight (minimum 0) :

Branch-length parameter mutation weight (minimum 0) :

Topology mutation weight (minimum 0) :

NNI mutation weight (minimum 0) :

SPR mutation weight (minimum 0) :

Localized SPR mutation weight (minimum 0) :

Max range for localized SPR topology changes (minimum 0) :

Mean # of branch lengths to change per mutation (minimum 0) :

Magnitude of branch-length mutations (50 to 2000) :

Magnitude of model parameter mutations (50 to 2000) :

Relative weight assigned to already attempted branch swaps (0.01 to 1.0) :

Relative weight assigned to branch swaps based on locality (0.1 to 10) :

Miscellaneous

Relative size of resampled data matrix (0.1 to 10) :

Infer ancestral states

Optimize input only (Do no tree searches!)