Seq-GenSimulates the evolution of nucleotide or amino acid sequences | |
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Seq-Gen Ranking & Summary
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- License:
- Freeware
- Publisher Name:
- Andrew Rambaut
- Operating Systems:
- Windows All
- File Size:
- 281 KB
Seq-Gen Tags
- simulator sequence acid Acid Titration nucleotide proportion acid font key code ACID transaction nucleic acid analysis nucleotide sequence nucleotide sequence manager nucleotide simulate evolution find amino acid amino acid finder search amino acid Amino Acid analyzer amino acid sequence amino acid amino acid translator acid theme extract amino acid acid solution amino acid residue optimal amino acid nucleotide substitution model nucleotide motif nucleic acid sequence nucleotide substitution nucleotide annotation nucleotide alignments analyze amino acid nucleic acid analyze amino acids pair amino acids pair analysis amino acid sequence analysis analyze amino acid sequence amino acid classification Amino Acid Topology evaluation simulator amino-acid detector detect amino-acid nucleotide polymorphisms nucleotide mutation nucleotide fraction analyze amino acid chain acid loops ACID transactions hotmail password cracker acid pro acid pro 7 games application english albania machine bubbles on line inkjet printer c3125 mobile text message aim pro for seq water glock 26 gen transformar iso em credit card gen sun practice exams umd gen
Seq-Gen Description
Seq-Gen was developed to be a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution. Seq-Gen is a command-line controlled program written in ANSI C. It should be easily compiled and run on any UNIX system or workstation. This paper describes the use of Seq-Gen on a UNIX machine. The application requires an amount of memory proportional to the size of each simulated sequence data set. Running Seq-Gen To run Seq-Gen you type: seq-gen < > where are the parameters for the program (described below), is the tree file and is the name of the file that will contain the simulated sequences. The tree file must contain one or more trees in PHYLIP format. The sequences produced by Seq-Gen are written to the standard output (and can thus redirected to the output file using > ). Other information and results are written to the standard error and thus will appear on the screen.
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