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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.38.2.
.TH SEQ-GEN "1" "March 2011" "seq-gen 1.3.3" "User Commands"
.SH NAME
seq-gen \- Sequence Generator
.SH SYNOPSIS
.B seq-gen
[\fI-m MODEL\fR] [\fI-l #\fR] [\fI-n #\fR] [\fI-p #\fR] [\fI-s # | \-d #\fR] [\fI-k #\fR][\-c #1 #2 #3 | \-a\fR # [\-g #]] [\-f e | #] [\-t # | \-r\fR #][\-z #] [\-o[p][r][n]] [\-w[a][r]] [\-x NAME] [\-q] [\-h] [treefile]
.SH DESCRIPTION
Sequence Generator \- seq\-gen
Version 1.3.3
.IP
.HP
\fB\-l\fR: # = sequence length [default = 1000].
.HP
\fB\-n\fR: # = simulated datasets per tree [default = 1].
.HP
\fB\-p\fR: # = number of partitions (and trees) per sequence [default = 1].
.HP
\fB\-s\fR: # = branch length scaling factor [default = 1.0].
.HP
\fB\-d\fR: # = total tree scale [default = use branch lengths].
.HP
\fB\-k\fR: # = use sequence k as ancestral (needs alignment) [default = random].
.IP
Substitution model options:
.HP
\fB\-m\fR: MODEL = HKY, F84, GTR, JTT, WAG, PAM, BLOSUM, MTREV, GENERAL
.IP
HKY, F84 & GTR are for nucleotides the rest are for amino acids
.HP
\fB\-a\fR: # = shape (alpha) for gamma rate heterogeneity [default = none].
.HP
\fB\-g\fR: # = number of gamma rate categories [default = continuous].
.HP
\fB\-i\fR: # = proportion of invariable sites [default = 0.0].
.IP
Nucleotid model specific options:
.HP
\fB\-c\fR: #1 #2 #3 = rates for codon position heterogeneity [default = none].
.HP
\fB\-t\fR: # = transition\-transversion ratio [default = equal rate].
.HP
\fB\-r\fR: #1 #2 #3 #4 #5 #6= general rate matrix [default = all 1.0].
.HP
\fB\-f\fR: #A #C #G #T = nucleotide frequencies [default = all equal].
.IP
Amino Acid model specific options:
.IP
specify using the order ARNDCQEGHILKMFPSTWYV
.HP
\fB\-r\fR: #1 .. #190 = general rate matrix [default = all 1.0].
.HP
\fB\-f\fR: #1 .. #20 = amino acid frequencies e=equal [default = matrix freqs].
.IP
Miscellaneous options:
.HP
\fB\-z\fR: # = seed for random number generator [default = system generated].
.HP
\fB\-o\fR: Output file format [default = PHYLIP]
.IP
p PHYLIP format
r relaxed PHYLIP format
n NEXUS format
.HP
\fB\-w\fR: Write additional information [default = none]
.IP
a Write ancestral sequences for each node
r Write rate for each site
.HP
\fB\-x\fR: NAME = a text file to insert after every dataset [default = none].
.HP
\fB\-h\fR: Give this help message
.HP
\fB\-q\fR: Quiet
.IP
treefile: name of tree file [default = trees on stdin]
.SH AUTHOR
(c) Copyright, 1996\-2004 Andrew Rambaut and Nick Grassly
Department of Zoology, University of Oxford
South Parks Road, Oxford OX1 3PS, U.K.
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