This is the command seq-gen that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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]
Use seq-gen online using onworks.net services
