![]() Once this has been extracted, inside the folder there will be a README file and another *.zip file. The download will be in the format of a *.zip file, and can be extracted by right clicking on this file, and clicking "Extract All" for Windows, or double clicking the folder for Mac. These following steps of extraction of the files seem tedious and repetitive, but they are necessary in order to maintain the file structure. This can be found by going to the top of this page, clicking the green button named "Code" and clicking the option "Download Zip". Once this Python shell is successfully installed, download the NSplitter file system from this GitHub repository. When downloaded, there will be a setup prompt to help set it up on your computer. This program is not specific to Windows or Mac, and only requires the download of the program and the presence of Python (steps detailed below).įor a benchmark, this program has compared an alignment of 20 sequences, each being 30,000 bases long, in under 10 seconds.įirst, Python must be installed. Please note that the program first converts all 'U's to 'T's, and therefore the output files will be of the T version of all codons. NSplitter also outputs a fourth file called 'position-values.txt' which contains a string of values, '0', '1' or '2', for each codon in the alignment '0' means that that codon position has no-differences in all the sequences, '1' means that there is at least one or more changes in that codon position, but all are silent, and '2' meaning that at least one of the changes in that codon position is non-silent irrespective of whether there are any silent changes too. ![]() These, like the input alignment are in FAS/FASTA/txt file format, allowing them to be opened by programs such as BioEdit and text editing software such as Microsoft Word and Notepad. ![]() ![]() It identifies the non-silent (non-synonymous), silent (synonymous) and unchanged codons, and outputs them in three separate files "ns", "s" and "u". NSplitter is a Python program which takes an alignment of the coding regions of a set of homologous genes or genomes. ![]()
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