Details: see Format Converter Explanation.In particular, we provide important details about some specific formats: phylip, SLX, Nexus, and raw.For descriptions of some common sequence formats, see Common Sequence Formats. Please write us if we are missing a format that you find useful, or if you find mistakes in our conversions. SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. Knowing nothing in life is free, I prefer to buy apps rather than download the free ones. In App store, the only real choice seemed to be 'The File Converter.' File Converter does not convert.msf files, I later learned.
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Convert among Alignment file formats (Nexus, phylip, fasta, etc.)2/14/2015 When I'm working with a dataset for phylogenetics, I often need to convert among different file formats. MrBayes requires nexus files, PhyML and RaxML require PHYLIP, many other programs need fasta files (just to name a few). Manually editing and converting among these file formats is easy enough to do, but it's also time consuming and may introduce human error. Instead, I like to use tools or scripts that automate the process. Here are my top choices: 1) ALTER (ALignment Transformation EnviRonment) This online tool can convert alignment files to and from the following formats: NEXUS (.nex), Fasta (.fa or .fasta), Phylip (.phy or .phylip), ALN, GDE, MEGA, MSF, PIR. It can be found at this address: http://sing.ei.uvigo.es/ALTER/ Simply upload your alignment file, select your output format, and convert. The converted file will download automatically to your computer. ALTER is incredibly easy to use, completely free, and does not require a software download. My only complaint is that the site goes down pretty frequently, so it's good to have one of these other options up your sleeve: 2) PGDSpider PGDSpider is a powerful java-based tool for file conversion that can be run either from command line or a GUI. 'PGD' stands for Population Genetics Data, so many of the file formats are common to population genetics data (microsats, SNPs, etc.) and software (Arlequin, Structure, etc.). PGDSpider is intuitive enough to use. It's not quite as simple as ALTER, but it's also much more powerful in terms of the number of file formats it can handle. It can parse 31 and write to 34 different file formats. The PGDSpider website notes that it is not capable of handling large NGS datasets, which may make this final option more appealing: 3) Custom scripts I'll be honest: I'm no good at writing code. However, I'm a ninja when it comes to finding other people's code online and tweaking it when necessary. A simple google search reveals many, many existing scripts for file format conversion in several different languages. A search for 'Perl convert fasta nexus' brought me to this script, and 'python convert nexus phylip' took me here. This is the path I usually take for file conversion with large datasets. There are a lot of other options out there (e.g. this online tool) but those listed above are the ones that I am most familiar with. What's your favorite? 9/11/2015 06:50:31 am I tried the file format conversion ALTER tool you suggested, but it looks like my file is just a little to large for the tool to handle. 9/11/2015 11:02:58 am Hi Jason, 9/11/2015 11:43:11 am It looks like the max size for http://www.ibi.vu.nl/programs/convertalignwww/ is 8.1 MB, my file is 8.8 12/25/2016 09:04:04 am Check this script for massive conversion python3 AMAS.py convert -d dna -f fasta -i *fas -u nexus 1/17/2016 03:22:51 pm Dear Dr. Everson, 1/20/2016 05:56:52 pm 'I'm attempting a multi-loci concatenation via Mr. Bayes and tried to use ALTER to format a Nexus file.' 1/29/2016 03:20:29 pm Formatting and Ambiguous characters: Yes, ALTER was able to convert my file once I had done the right formatting. This also corrected my issue with ambiguous characters. Thank you. 3/10/2016 10:40:39 pm Dear Katie 1/30/2018 11:00:52 am Thank you for the very helpful post. I actually want to convert from fastq to phy. ) have so many files and they are large for ALTER. Do you have any thoughts? Thanks! 2/1/2018 03:24:01 pm I haven't used this website before but it seems promising! http://sequenceconversion.bugaco.com/converter/biology/sequences/ Leave a Reply. |