Index

• --blstdev: Output Options
• --code: Data Options
• --codesfile: Data Options
• --empirical: Model Options
• --equalprobs: Model Options
• --fixedprobs: Model Options
• --freqs: Running Options
• --initpars: Starting Options
• --initparsfile: Starting Options
• --initprobs: Starting Options
• --justbl: Model Options
• --mask: Model Options
• --maskfile: Model Options
• --mixfile: Model Options
• --mixstring: Model Options
• --mixture: Model Options
• --model: Model Options
• --modelfile: Model Options
• --noautobackup: Running Options
• --nomask: Model Options
• --numpars: Model Options
• --observedinformation: Output Options
• --output: Output Options
• --parameterselection: Model Options
• --parsimony: Starting Options
• --path: Running Options
• --printsitelikes: Output Options
• --recover: Running Options
• --setfixedpars: Model Options
• --showeverysite: Debugging and Status Options
• --simulate: Running Options
• --state: Running Options
• --testderivs: Technical Options
• --treenumber: Data Options
• --tstats: Output Options
• --usematrix: Model Options
• --variables: Starting Options
• --variableselect: Running Options
• --varprobs: Model Options
• -b: Technical Options
• -D: Debugging and Status Options
• -d: Data Options
• -e: Technical Options
• -f: Data Options
• -f option, details: Changing the Search Path
• -i: Debugging and Status Options
• -m: Starting Options
• -n: Running Options
• -o: Technical Options
• -P: Technical Options
• -p: Model Options
• -q: Debugging and Status Options
• -T: Technical Options
• -t: Data Options
• -v: Debugging and Status Options
• adding matrices: summats
• alignment gaps, removing: stripambiguous
• ambiguous data, removing: stripambiguous
• angle between steepest and actual ascent: Status and Debugging Output
• automatic backup, disable: Running Options
• backup: Running Options
• backup, disable automatic: Running Options
• branch lengths, optimising only: Model Options
• branch lengths, standard deviation: Output Options
• branch lengths, use values from file: Starting Options
• changing default values: Configuration
• code, file: Data Options
• code, genetic: Data Options
• codon order: reordermatrix
• cold: Invoking Cold
• command not found, installation: Troubleshooting
• commandline options: Invoking Cold
• commandline options, specifying from a file: Starting Options
• commandline options, specifying in a file: Variables
• compilation: Installation
• compiling individual programs: Make Targets
• configuration: Installation
• constant matrix: Model Options
• constant parameters, setting values: Model Options
• converge, failed to: Running Options
• converting matrices from other sources: reordermatrix
• could not find file: Running Options
• data file, format: Data
• data file, tree file, simultaneous selection: Data Options
• data file, using: Data Options
• data options: Data Options
• data, simulating: Running Options
• debugging aborted programs: State File
• debugging derivatives: Technical Options
• debugging options: Debugging and Status Options
• debugging output: Status and Debugging Output
• debugging output, controlling: Debugging and Status Options
• default values, changing: Configuration
• derivatives, testing: Technical Options
• disable automatic backup: Running Options
• displaying site likelihoods: Output Options
• DNA sequence: Data
• empirical pi values: Model Options
• equal mixing probabilities: Model Options
• errors, automatically stop program: Debugging and Status Options
• errors, installation: Troubleshooting
• expected improvement: Status and Debugging Output
• failed to converge: Running Options
• faster processing: Technical Options
• file format: File Format
• file searching, details: File Searching
• file, commandline options file format: Variables
• file, data: Data
• file, genetic code: Data Options
• file, initial parameters: Initial Parameters
• file, matrix format: Matrices
• file, mixture: Mixture
• file, model: Models
• file, output: Output Options
• file, searching for: Running Options
• file, selecting data and trees files together: Data Options
• file, selecting data file: Data Options
• file, selecting tree file: Data Options
• file, sequence: Data
• file, setting commandline options from: Starting Options
• file, state: State File
• file, tree: Trees
• final output: Final Output
• Fisher information matrix: Output Options
• format of files: File Format
• formatting output: Output Templates
• frequencies, setting for simulations: Running Options
• gaps, removing alignment: stripambiguous
• genetic code: Data Options
• genetic code file: Data Options
• getting started: Installation
• information matrix, observed: Output Options
• initial parameter values, use matrix to set: Starting Options
• initial parameters: Initial Parameters
• initial value options: Starting Options
• input files: File Format
• installation problems: Troubleshooting
• installing cold: Installation
• interactive mode,: Debugging and Status Options
• interrupted program execution: Running Options
• Invoking Cold: Invoking Cold
• iterations, number of: Running Options
• license: GNU Free Documentation License
• likelihood, output site: Output Options
• log file: Debugging and Status Options
• macros, changing values: Configuration
• make errors: Troubleshooting
• make file: Installation
• make options: Make Targets
• mask matrix: Model Options
• matrices, forming new: summats
• matrices, reading from vectors: readmatricesfromcols
• matrix format in files: Matrices
• matrix, constant: Model Options
• matrix, mask: Model Options
• matrix, observed information: Output Options
• matrix, reorder rows and columns: reordermatrix
• matrix, use to set initial parameter values: Starting Options
• menu, displaying menus: Debugging and Status Options
• minimising likelihood: Technical Options
• mixed model: Model Options
• mixing probability, constant: Model Options
• mixing probability, equal: Model Options
• mixing probability, number variable: Model Options
• mixture file format: Mixture
• mixture file, selecting: Model Options
• mixture string format: Mixture
• mixture, equal mixing probability: Model Options
• mixture, mixing probability: Model Options
• model file format: Models
• model file, using: Model Options
• model matrix, converting to list of matrices: readmatricesfromcols
• model options: Model Options
• model selection, t statistic: Output Options
• model selection, using cold for model selection: Running Options
• model, mixed: Model Options
• model, using: Model Options
• modulus: Status and Debugging Output
• multi-threaded: Technical Options
• multiple cores: Technical Options
• new matrices: summats
• Newton-Raphson, number of iterations: Running Options
• non-interactive mode: Debugging and Status Options
• number of iterations in optimisation: Running Options
• number of threads, how to decide: Number of Threads
• number of variable mixing probabilities: Model Options
• observed information matrix: Output Options
• optimisation options: Running Options
• optimisation, just branch lengths: Model Options
• optimisation, number of iterations: Running Options
• options, data: Data Options
• options, debugging and status: Debugging and Status Options
• options, initial values: Starting Options
• options, model: Model Options
• options, optimisation: Running Options
• options, output: Output Options
• options, running: Running Options
• options, specifying from a file: Starting Options
• options, specifying in a file, format: Variables
• options, starting: Starting Options
• options, technical: Technical Options
• order of codons: reordermatrix
• output: Output
• output file: Output Options
• output options: Output Options
• output site likelihoods: Output Options
• output template: Output Templates
• output, final: Final Output
• output, formatting: Output Templates
• output, suppressing output while running: Debugging and Status Options
• parallel processing: Technical Options
• parameter selection, automatic: Running Options
• parameters: Model Options
• parameters, initial: Initial Parameters
• parameters, setting values of constant: Model Options
• parsimony: Starting Options
• path: Running Options
• pi values, empirical: Model Options
• prevent automatic backup: Running Options
• probability, mixing, number variable: Model Options
• processors, using multiple: Technical Options
• program output: Output
• programs, utility: Utilities
• progress, show site number: Debugging and Status Options
• readmatricesfromcols: readmatricesfromcols
• recover from interrupted program execution: Running Options
• remove ambiguous sites: stripambiguous
• reordermatrix: reordermatrix
• resume interrupted program execution: Running Options
• running options: Running Options
• search path: Running Options
• searching order for files: File Searching
• select parameters: Model Options
• sequence file, format: Data
• simulation: Running Options
• simulation, setting frequencies: Running Options
• single-threaded: Technical Options
• site likelihoods, displaying: Output Options
• sites, removing ambiguous: stripambiguous
• standard deviation of branch lengths: Output Options
• start from last point found on previous execution: Running Options
• starting options: Starting Options
• starting parameter values, use matrix to set: Starting Options
• starting parameters: Initial Parameters
• state file format: State File
• state file, setting: Running Options
• statistic, t: Output Options
• status options: Debugging and Status Options
• status output: Status and Debugging Output
• status, partial hessian calculation: Debugging and Status Options
• step number: Status and Debugging Output
• step size: Status and Debugging Output
• strip ambiguous sites: stripambiguous
• stripambiguous: stripambiguous
• summats: summats
• symmetric matrices, reading from vectors: readmatricesfromcols
• t statistic: Output Options
• technical options: Technical Options
• template: Output Templates
• testing derivatives: Technical Options
• threads, deciding number of: Number of Threads
• threads, setting number of: Technical Options
• tree file, data file, simultaneous selection: Data Options
• tree file, format: Trees
• tree file, use branch lengths from: Starting Options
• tree file, using: Data Options
• troubleshooting, installation: Troubleshooting
• uninstall: Make Targets
• user input: Debugging and Status Options
• utilities, compiling seperately: Make Targets
• utility programs: Utilities
• variable correlation: Output Options
• variable file: Variables
• variable file, use: Starting Options
• variable selection, t statistic: Output Options
• variable selection, using cold for variable selection: Running Options
• variance of branch lengths: Output Options
• warnings, automatically continue: Debugging and Status Options
• warnings, showing: Debugging and Status Options
• warnings, suppressing: Debugging and Status Options