Cipres Science Gateway

HELP

New users: Please review our current fair use policy.

Basic CIPRES Science Gateway Usage:

The CIPRES Science Gateway is designed to manage data much like an e-mail client. The data is then used to stage indivudal jobs.
Here we provide some flash demos to illustrate the basic functionalities of the CIPRES Science Gateway. Each demo is less than 3 minutes.

Known Issues: here.

Supported Formats:

We provide support interconversion of many file formats with the tools Readseq and NCL Converter. At this moment, files must be provided in the formats known by the tool. Typically a tool has one or two formats that are accepted as input, and we rely on the user to provide data in the correct format. We intend to provide an interconversion service in the not-too-far distant future.
NCL Converter is the prefered tool for converting NEXUS files to relaxed Phylip format (as required for RAxML). READSEQ is not reliable for parsing Nexus into other formats.On the other hand, the Normalized Nexus produced by NCL Converter is not recognized by MrBayes, because characters and taxa are broken into separate blocks. Normalized Nexus headers look like this:

#NEXUS
begin taxa;
dimensions ntax=12;
taxlabels a b c d e f g u v x y t; end
begin characters;
dimensions nchar=432;
format datatype=dna missing=?;
matrix

MrBayes 3.1.2 expects characters and taxa to be in a single data block, like this:

#NEXUS
begin data;
dimensions ntax=12 nchar=432;
format datatype=dna missing=? gap=-;
matrix

This can be corrected manually with a text editor.

Documentation of some common formats is provided below. The text has been liberally borrowed from a variety of sources.

NEXUS

Phylip

Hennig86

FASTA (fasta; multiple fasta; aligned fasta)

CLUSTAL

IUPAC Amino Acid and Nucleic Acid symbols

If there is a tool or a feature you need, please let us know.