Make a copy of the fasta file and paste it into the ruby directory (C:\ruby). Right click on the new shortcut, select properties, change start in to c:\ruby, hit ok and you are done. Right click in the ruby directory, new, shortcut, enter cmd, hit next, hit finish. In the ruby directory I create a shortcut to a command prompt that opens in this directory.
#BIOEDIT CONVERT TXT TO FASTA INSTALL#
I install ruby in the directory C:\ruby (from memory you should avoid installing it in directories with spaces in the name). I use scripts written by Simon Berger available from that use ruby. MEGA will prompt you if there are any errors so you can fix them. Close the file in Word, double click it and it should open in MEGA.
#BIOEDIT CONVERT TXT TO FASTA SOFTWARE#
Save the file as a txt file with the extension of meg (make sure that your version of Windows is set to show the file extensions ( ) so that you can see if the extension is correct as the software will often put another extension on the file that you cannot see. To create a MEGA file from the fasta file search and replace in word (control-h) for > and replace with #, make a mental note of how many replacements were made.Ĭopy and paste this header (or one from one of your previous MEGA files), change the values in yellow to suit your situation. Right click the fasta file and open it in Microsoft Word (or any editing software that will save a txt file). Be sure that BioEdit is saving it in fasta format too (e.g., use the save as rather than the save option the first time you save it) as BioEdit does not automatically change any file extensions, you have to manually do that when you save the file. Check that the sequences are all aligned and ok.
![bioedit convert txt to fasta bioedit convert txt to fasta](https://sumrandee.files.wordpress.com/2009/12/after-file-open.jpg)
You must have the data in this format for these instructions to work! Open the fasta file in BioEdit.
![bioedit convert txt to fasta bioedit convert txt to fasta](https://wiki.bits.vib.be/images/a/af/Bioeditalign.png)
BioEdit saves fasta formatted files with the sequence name on the first line and the entire sequence on the second line (with no hard returns until the end). Which program you use shouldn’t matter as long as it creates fasta files in the same format as presented here. I use BioEdit for managing my sequence data. My preference is to start with a fasta format file and convert that to various other formats.
![bioedit convert txt to fasta bioedit convert txt to fasta](https://i1.rgstatic.net/ii/profile.image/819678163263488-1572437911173_Q512/Valeria-Faggioli.jpg)
Output from modeltest containing the model scores Output from paup for obtaining model scores Simply sorting by date many not work if you are actively working with several of the files.īirdshead = group of interest, cb = gene abbreviation Inevitably you will find errors and have to go back and update/change files as well, thus add something to the name to make that clear (e.g., final, fixed.july.7, etc.). You will potentially end up with many many files for different analyses that you do and it is critical to be able to identify which is which. I start with the taxon or group of interest, the gene and then what is in the content of the file. This is typical of what I have, although I usually end up with many more.
![bioedit convert txt to fasta bioedit convert txt to fasta](http://www.peter.unmack.net/molecular/data/sequence.names.excel.gif)
It is good to develop a standard naming system for files. Irrespective of that, PAUP is also great to use for editing data files as it keeps all the data on a single line (whereas Word wraps it) and it handles copying and pasting and searching and replacing quite nicely. The only one I’ve seen that comes close to being nice is the new version of PAUP. Most programs that I have examined for importing and exporting different file formats always seem to introduce artifacts or problems that annoy me. If you first need to concatenate multiple data files together see the section at the end first. There are many different ways to go back and forth between different file formats. Data file manipulation Data file manipulationīy Peter Unmack How do you take your sequence data and format it for analysis?