Getting Started with readAl v1.2

Thank you for choosing readAl v1.2 to convert your alignments. You will see that it is very easy to get familiar with the program. The first thing you need to do to start is decide whether you will be using readAl in its command line version or through the web interface.

The command line version is faster and has more possibilities, so it is recommended if you are going to use readAl extensively. The readAl webserver included in Phylemon 2.0 provides a friendly user interface and the opportunity to concatenate your trimmed alignment to many different phylogenetic analysis.

Input and Output formats

readAl reads protein or nucleotide alignments in several Multiple Sequence Alignment formats, including Phylip, Fasta, Clustal, NBRF/Pir, Mega and Nexus. The program detects automatically the input format and converts the alignment to other available formats. Moreover, the program can extract information about the alignment using the -format or/and -type options. The first one returns the input alignment format and its type (“single” for files with a single alignment or “multi” for files with more than one alignment). The second options is related to alignment type (“aminoacids” or “nucleotides”).

Command line version

Basic usage

   readal -in <inputfile> -out <outputfile> -(format options).

Common options

   -h                       Prints this information and show some examples.
   --version                Prints the readAl version.

   -in <inputfile>          Input file in several formats (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip, mega).
   -out <outputfile>        Output alignment in the same input format (default stdout).

   -format                  Prints the the input file format (fasta, clustal, ...) and kind (single or multi).
   -type                    Prints the input file type (Nucleotides or Amino Acids).

   -clustal                 Output file in CLUSTAL format
   -fasta                   Output file in FASTA format
   -nbrf                    Output file in NBRF/PIR format
   -nexus                   Output file in NEXUS format
   -mega                    Output file in MEGA format
   -phylip3.2               Output file in PHYLIP3.2 format
   -phylip                  Output file in PHYLIP/PHYLIP4 format


1) Converts an input file to fasta format.

   trimal -in <inputfile> -out <outputfile> -fasta

2) Gets information from a given alignment.

   trimal -in <inputfile> -type -format

Allowed combination

It is impossible to convert a given input file and, at the same time, gets information about that file.

Webserver version

readAl v1.2 has been implemented in the new Phylemon webserver version, an online platform for phylogenetic and evolutionary analyses of molecular sequence data. The readAl webserver included in Phylemon provides a user friendly interface and the opportunity to concatenate your trimmed alignment to many different phylogenetic analyzes.

You can open an account in Phylemon, this will allow you to store your data for future sessions. If you do not want to open a user account, just log in as an anonymous user.

You can start by uploading the alignment to be converted by using the “select file from your machine” option, this will open a file browser on your computer. Alternatively, you can select one alignment from a previous phylemon session, use one of the examples available or paste your alignment.

Once the alignment is uploaded, you need to select the new alignment format among the available ones. Finally, you can give a “job name” to your job in order to reuse the result of this process in other session.

use_of_the_readal_v1.2.txt · Last modified: 2009/04/19 20:25 by scapella
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