DISTMAT : Creates a distance matrix from multiple alignments (EMBOSS)

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input Section

advanced Section

output Section

input Section

msf -- gapany [set of sequences] (-msf) : please enter either :

the name of a file:
or the actual data here:

(sequence format)

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Method to use -- Multiple substitution correction methods for nucleotides (-nucmethod)
Method to use -- Multiple substitution correction methods for proteins (-protmethod) ? Uncorrected Jukes-Cantor Kimura Protein
Use the abiguous codes in the calculation. (-ambiguous)
Weight given to gaps (-gapweight)
Base position to analyse. (-position)
Calculate the a-parameter (-calculatea)
a-parameter (-parametera)

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output Section

Enter a name for the distance matrix (-outf)

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Some explanations about the options

input Section
msf -- gapany [set of sequences] (-msf): File containing a sequence alignment.
enter either the name of a file or the actual data: if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button); OR you can type your data in the next area, or cut and paste it from another application.; (but not both)
advanced Section
Method to use -- Multiple substitution correction methods for nucleotides (-nucmethod): Multiple substitution correction methods for nucleotides.
Method to use -- Multiple substitution correction methods for proteins (-protmethod): Multiple substitution correction methods for proteins.
Use the abiguous codes in the calculation. (-ambiguous): Option to use the abiguous codes in the calculation of the Jukes-Cantor method or if the sequences are proteins.
Weight given to gaps (-gapweight): Option to weight gaps in the uncorrected (nucleotide) and Jukes-Cantor distance methods.
Base position to analyse. (-position): Choose base positions to analyse in each codon i.e. 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases.
Calculate the a-parameter (-calculatea): This will force the calculation of the a-parameter in the Jin-Nei Gamma distance calculation, otherwise the default is 1.0 (see -parametera option).
a-parameter (-parametera): User defined a parameter to be use in the Jin-Nei Gamma distance calculation. The suggested value to be used is 1.0 [Jin et al.] and this is the default.
Sequence format: The sequence will be automatically converted in the format needed for the program; providing you enter a sequence either:; in plain (raw) sequence format or in one of the following known formats:; IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW; You may enter in the text area a database entry code, or an accession number, in this form:
database:entry_name
or:
database:accession.

Pise form generator version: 5.a (16 Dec 2002 11:53)