RAT:Recombination Analysis Tool Crack Activation Free 2022 [New]

RAT:Recombination Analysis Tool is a simple, easy to use, Java application designed to offer you an uncomplicated and intuitive tool for high-throughput, distance-based analysis of both DNA and protein multiple sequence alignments, in any one of seven different file formats.
All of RAT’s operations are carried out through GUI’s, and all output can be saved as data files (.txt, .xls, .csv), or .jpg files in the case of graphical outputs. RAT is intuitive and easy to use, and only requires a minimum of input from the user. All the parameters have default values, all of which may be changed by the user.

RAT:Recombination Analysis Tool Crack+ Download

o — Application
o — Distance-based methods for recombination analysis
o — Can detect recombination events in recombinant DNA sequences
o — Measures the similarity between two DNA sequences using the BLASTN and BLASTX algorithms
o — Detects and displays similar non-homologous DNA sequences within a DNA sequence
o — Detects and displays similarities between proteins, and also some general alignment procedures (requiring AlignACE and GeneDoc)
o — Used to detect genes with recombination events, and to calculate the numbers of genes with recombination events that are present in both a «parental» and «child» gene
o — Detects known hotspots/coldspots
o — Can use average, maximum, minimum, and/or variance methods for distance estimation
o — Uses ‘PEDAGOGIC’, an improved diamond protocol
o — Input data can be either.xml,.tsv, or.xls files, where each line corresponds to a sequence (which can be either DNA or protein)
o — Can be used for DNA sequence or protein sequence analysis
o — Allows the user to specify the file location for both the input and output files
o — Can be used with the BSD, MySQL or MS-SQL databases, either directly or through ODBC
o — Graphical outputs are supported in.jpg,.png and.emf files, and can be viewed as a window on your computer screen
o — Large alignment files can be viewed graphically in.png and.emf files
o — A bookmark system is supported
o — Supports multiple files
o — RAT allows simultaneous analysis of many different sequences
o — Includes a command line interface
o — Available for Linux, Windows and Mac OS X platforms
o — Support for different versions of Java JDK, JRE, and J2EE
o — Also a number of applets for RAT.
System Requirements:
— Java 1.3, Java 1.4 or Java 5 or higher
— MS-SQL JDBC Driver —
— ODBC — MS-SQL driver —
— MySQL JDBC Driver —
— MySQL JDBC Driver —
— XML 2.0 Pars

RAT:Recombination Analysis Tool

The RAT Annotator allows you to view, annotate, cluster and analyse proteins, peptides or DNA sequences. It uses MSAviewer for display.
RAT Annotator can be used to the following tasks:
• Annotate DNA or protein sequences by marking all the recombinant regions in the multiple sequence alignment, whether the break is caused by transposon, retroposition, segmental duplication or any other mechanisms that leads to sequence divergence.
• Cluster protein or DNA sequences based on their similarity, using BLAST or RANKPEP algorithms.
• Cluster protein or DNA sequences based on their similarity, using BLAST or RANKPEP algorithms.
• Run ClustalW, ClustalW2, ClustalX, Gaudin, ClustalP, MSPLIT, or DIALIGN on Protein or DNA sequences or their ‘MSA’ representations
• Detect potential recombination events across the multiple sequence alignment of a protein or DNA sequence and its ‘MSA’ representation.
• Construct a «Break-point graph» to show clusters of recombination events between a particular protein or DNA sequence and its ‘MSA’ representation.
• Draw a «Break-point graph» to show clusters of recombination events between a particular protein or DNA sequence and its ‘MSA’ representation.
• Mark recombination regions within a protein or DNA sequence sequence and its ‘MSA’ representation.
• Calculate the average number of base pairs between (A, C, G, T) nucleotides which are recombinants with respect to (A, C, G, T) bases of the region including the nucleotide.
• Calculate the average number of base pairs between (A, C, G, T) bases which are recombinants with respect to (A, C, G, T) nucleotides of the region.
• Use the JUMPLABEL tool to determine the precise recombination break point of any given recombination region.
• Rotate the display of the multiple sequence alignment in 180 degrees.
• Make vectorial images of the graphic outputs of RAT, either in JPEG, or PostScript formats.
• Make postscript in terms of multiple sequence alignment and a break-point graph.
• Export ‘MSA’ file to ClustalW or ClustalW2 format.
• Export graphic output to the specified format.
• Export graphic output
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RAT:Recombination Analysis Tool Crack+ License Code & Keygen Download X64

It is designed to offer you an uncomplicated and intuitive tool for high-throughput, distance-based analysis of both DNA and protein multiple sequence alignments, in any one of seven different file formats.
All of RAT’s operations are carried out through GUI’s, and all output can be saved as data files (.txt,.xls,.csv), or.jpg files in the case of graphical outputs. RAT is intuitive and easy to use, and only requires a minimum of input from the user. All the parameters have default values, all of which may be changed by the user.
RAT:Recombination Analysis Tool is written in Java and is OS independent.
Standard Input: Whole genome alignment or gene alignment (amino acid or nucleotide) file.
Standard Output: Alignment, distance, DNAdist, COVDist, FitchT, Popper, Recombination width (Rw), Recombination distance (Rr), and Matrix.

… including «known markers», «genetic markers», «known genetic markers», «genetic markers», «single-nucleotide polymorphism», «SNP’s», «SNP’s», «macromolecular markers», «macro markers», «positional candidate gene maps», «candidate gene maps», «candidate gene maps», «candidate gene map», «candidate gene maps», «locus maps», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «loci», «l

What’s New in the RAT:Recombination Analysis Tool?

RAT is a Java application that offers a simple and straightforward way to analyze DNA or protein alignments in a non-traditional way. It is part of a family of programs: RAT:Recombination Analysis Tool, RAT:Recombination Analysis Tool Light, and RAT:Recombination Analysis Tool Lite.
RAT runs on Windows, Mac, and UNIX platforms, and doesn’t require the use of additional packages. RAT is able to read and write in all the seven different file formats: Arial, Computers, Ipsum, MS Word, Plain Text, TAR, and PDF.
RAT allows you to graphically represent the results of all its analyses, and to save the plots in.jpg format. The alignments can be represented by default in their linear or circular graphic, or in their distance matrix.
You can easily find data with recombination rates from the set of proteins (or DNA sites) that you choose, and you can obtain an estimate of the recombination rate for each alignment-pair. RAT can detect recombination in 6 (protein) or 16 (DNA) species simultaneously, and, although not as intuitive, it also allows you to search for recombination in any other species.
Another interesting feature of RAT is its ability to analyze asymmetric data (multispecies), and create new species from selected species. And, finally, you can easily create new alignments from file formats in which it is not possible to read and write, or create new alignments from multiple alignments.

TIP: In most of the situations we use about 6,000 bacteria protein sequences to calculate the recombination rate per pair of proteins.

CRH:Co-Roots and Hollingsworth
The co-rooted haplotype network analysis produces visual representations of the genetic relationships among haplotypes of a pair of closely related species and/or population samples. This is a very useful tool in studies of population divergence, phylogenetic relationships, genetic exchange, and/or dispersal events.
The tool is an extension of the haplotype network analysis described by Templeton et al. (2003). The co-rooted haplotype network uses the same algorithm for identifying haplotypes, but then uses another algorithm (identical to the one used by Templeton et al. 2003) to identify two new haplotypes and their possible connections. This step is performed for all sites in the alignment. If multiple haplotypes are retrieved for a site,

System Requirements For RAT:Recombination Analysis Tool:

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Hard Drive: 5 GB available space
Recommended
PC Minimum: Intel Core i3 2.4 GHz or better

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