SYNOPSIS

seq-gen [-m MODEL] [-l #] [-n #] [-p #] [-s # | -d #] [-k #][-c #1 #2 #3 | -a # [-g #]] [-f e | #] [-t # | -r #][-z #] [-o[p][r][n]] [-w[a][r]] [-x NAME] [-q] [-h] [treefile]

DESCRIPTION

Sequence Generator - seq-gen Version 1.3.3

-l: # = sequence length [default = 1000].

-n: # = simulated datasets per tree [default = 1].

-p: # = number of partitions (and trees) per sequence [default = 1].

-s: # = branch length scaling factor [default = 1.0].

-d: # = total tree scale [default = use branch lengths].

-k: # = use sequence k as ancestral (needs alignment) [default = random].

Substitution model options:

-m: MODEL = HKY, F84, GTR, JTT, WAG, PAM, BLOSUM, MTREV, GENERAL

HKY, F84 & GTR are for nucleotides the rest are for amino acids

-a: # = shape (alpha) for gamma rate heterogeneity [default = none].

-g: # = number of gamma rate categories [default = continuous].

-i: # = proportion of invariable sites [default = 0.0].

Nucleotid model specific options:

-c: #1 #2 #3 = rates for codon position heterogeneity [default = none].

-t: # = transition-transversion ratio [default = equal rate].

-r: #1 #2 #3 #4 #5 #6= general rate matrix [default = all 1.0].

-f: #A #C #G #T = nucleotide frequencies [default = all equal].

Amino Acid model specific options:

specify using the order ARNDCQEGHILKMFPSTWYV

-r: #1 .. #190 = general rate matrix [default = all 1.0].

-f: #1 .. #20 = amino acid frequencies e=equal [default = matrix freqs].

Miscellaneous options:

-z: # = seed for random number generator [default = system generated].

-o: Output file format [default = PHYLIP]

p PHYLIP format r relaxed PHYLIP format n NEXUS format

-w: Write additional information [default = none]

a Write ancestral sequences for each node r Write rate for each site

-x: NAME = a text file to insert after every dataset [default = none].

-h: Give this help message

-q: Quiet

treefile: name of tree file [default = trees on stdin]

AUTHOR

(c) Copyright, 1996-2004 Andrew Rambaut and Nick Grassly Department of Zoology, University of Oxford South Parks Road, Oxford OX1 3PS, U.K.