All Commands

All Available Commands (v 3.1 specific)

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Show list of available commands

Accuracy

Compare values in a family to input from a file provided by the user.

Branchlength

Specify new branch lengths for the tree. Requires the tree command to be called first. Values are read from a file if an argument is given, otherwise the values are read from standard input.

Cvfamily

Cross validation by family. Tree, Load, and Lambda commands must be called first. Requires the number of folds??

Cvspecies

Cross validation by species

Date

Echoes the current date to output

Echo

Echoes the given text to output

Errormodel

Apply error correction to the data. Allows setting an error model from a file. Arguments: -sp, -model, -all. Tree and Load commands must be called first.

Esterror

Estimates error matrix from multiple data sets. Writes estimated errors to a file? [-dataerror file1 file2] or [-dataerror file1 -datatrue file2] -o outfile.\n

Exit

Exit back to the command line

Extinct

Runs a simulation. –t parameter gives the number of trials. Logs the total number of extinct families?

Family

Modify the families loaded by the “load” command in various ways. Arguments: • -idx • -id • -add • -del • -filter

Gainloss

Write the gains and losses for a specific family on each node of the tree

Genfamily

Generate simulated data

Info

Log information about the current state of the application: the gene family information; the tree (in Newick format); the lambda values and other data.

Lambda

Find or specify birth-death parameter

Lambdamu

Find or specify separate birth and death parameters

Lhtest

Compare likelihoods of lambda models

load

Data file and run parameters

log

Log output

Noerrormodel

Removes applied error models

Pvalue

Gets or sets the pvalues?? Or allows changing them on the fly

Quit

Exit the application

Report

Generate various reports on the data. The first argument will be the name of the file to use. Other arguments can appear in any order and may be:

• save
• branchcutting
• likelihood
• lh2

Retrieve

Restore program state from a file

Rootdist

Specify root family size distribution for simulation

Save

Store program state to a file

Score

Prints cluster membership

Simerror

Simulate or add error to the data based on errormodel

Simextinct

Runs a Monte Carlo simulation against the data and reports the number of extinctions that occurred.

Source

Run shell script specified by the file argument

Tree

Phylogenetic tree

Version

Print version information

Viterbi

choose the maximum likelihood across all possible inner nodes ??