seq-gen − Sequence Generator
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]
Sequence Generator − seq−gen Version 1.3.3
−l: # = sequence length [default = 1000]. |
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−n: # = simulated datasets per tree [default = 1]. |
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−p: # = number of partitions (and trees) per sequence [default = 1]. |
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−s: # = branch length scaling factor [default = 1.0]. |
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−d: # = total tree scale [default = use branch lengths]. |
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−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]. |
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−g: # = number of gamma rate categories [default = continuous]. |
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−i: # = proportion of invariable sites [default = 0.0]. |
Nucleotid model specific options:
−c: #1 #2 #3 = rates for codon position heterogeneity [default = none]. |
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−t: # = transition−transversion ratio [default = equal rate]. |
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−r: #1 #2 #3 #4 #5 #6= general rate matrix [default = all 1.0]. |
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−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]. |
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−f: #1 .. #20 = amino acid frequencies e=equal [default = matrix freqs]. |
Miscellaneous options:
−z: # = seed for random number generator [default = system generated]. |
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−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]. |
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−h: Give this help message |
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−q: Quiet |
treefile: name of tree file [default = trees on stdin]
(c) Copyright, 1996−2004 Andrew Rambaut and Nick Grassly Department of Zoology, University of Oxford South Parks Road, Oxford OX1 3PS, U.K.