This section first starts off with some quick useful commands that will be helpful to assess and manipulate your fasta and fastq file. Below are just two on the most useful ones that I like (I tend to like the command line interface ones, as they can easily be upscaled and used on your VM/supercomputer if needed). Some use the command line interface, there is also plenty of GUI and web-based programs too. This is to cover off on some basic quick command line tools to work with sequence data (mainly written for fasta and fastq format but generally useful for most types of sequence files. Quick commands for manipulating sequence files Muscle -maketree -in seqs_muscle.afa -out seqs_muscle_tree.phy -cluster neighborjoining Make an alignment and save to a file in FASTA format: In most cases, only a few command line options are needed. ![]() ![]() MUSCLE is one of the most common tools to align sequences. It has a range of features and plugins that allow you to do a wide range of phylogenetic and bioinformatic analysis.
0 Comments
Leave a Reply. |