Business and Investing Software Reviews – Guru Software. There is one side note at the time of this writing: Microsoft’s MSXML 3. 0 you are going to have to use the original version, which shouldn’t be a problem for most applications. If you’ve been keeping up binary option guru versions of Internet Explorer, you probably have some version of MSXML installed.
If you need to install it, you can either install the latest version of MDAC or the MSXML component itself. We’ll continue our investigation of XMLHTTP’s capabilities in Part 2 of this article! This compensation may impact how and where products appear on this site including, for example, the order in which they appear. Send me an e-mail if you would like to be notified of new releases. 1 Introduction MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences.
A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that give the best average accuracy in our tests. 2 Quick Start The MUSCLE algorithm is delivered as a command-line program called muscle. If you are running under Linux or Unix you will be working at a shell prompt.
If you don’t know how to use command-line programs, you should get help from a local guru. 1 Installation Copy the muscle binary file to a directory that is accessible from your computer. If you are using Windows, then the binary file is named muscle. From now on muscle should be understood to mean “muscle if you are using Linux or Unix, muscle. 2 Making an alignment Make a FASTA file containing some sequences. If you are not familiar with FASTA format, it is described in detail later in this Guide. For now, just to make things fast, limit the number of sequence in the file to no more than 50 and the sequence length to be no more than 500.
You should see some progress messages. If muscle completes successfully, it will create a file seqs. This is just like regular FASTA except that gaps are added in order to align the sequences. The default settings are designed to give the best accuracy, so this may be all you need to know. A good compromise between speed and accuracy is to run just the first two iterations of the algorithm. On average, this gives accuracy equal to T-Coffee and speeds much faster than CLUSTALW. 4 Fastest speed If you want the fastest possible speed, then the following example shows the applicable options for proteins.