NAME

       seq-gen - Sequence Generator

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.